Publications using or citing
AceView (alias Acembly)
Last partial update
March 12th, 2008
|
Year |
Publications using AceView |
Cumulative |
|
To march 2008 |
8… |
192… |
|
2007 |
35 |
184 |
|
2006 |
41 |
149 |
|
2005 |
34 |
108 |
|
2004 |
30 |
76 |
|
2003 |
24 |
46 |
|
2002 |
7 |
22 |
|
2001 |
12 |
15 |
|
2000 |
3 |
3 |
192- Garrett-Mayer E, Parmigiani G, Zhong X,
Cope L, Gabrielson E.
Cross-study validation and combined analysis of gene
expression microarray data.
Biostatistics. 2008 Apr;9(2):333-54. Epub 2007 Sep 14.
PMID: 17873151
191- Transcriptome
sequencing of malignant pleural mesothelioma tumors.
CONTEXT: We also conducted stringent MegaBLAST searches of reads that did not map to the 19,306 Known RefSeq Genes against the 52,935 “Main Genes” in AceView (www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html), the human genome, and the Pan troglodytes (chimpanzee) genome.
Note: Table 4 in
supplement material is the most interesting with respect to AceView and how
much better one accounts for the transcriptome in AceView than in RefSeq.
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3521-6. Epub 2008 Feb 26.
PMID: 18303113
190- HTLV-1 Integration into Transcriptionally Active
Genomic Regions Is Associated with Proviral Expression and with HAM/TSP.
Meekings
KN, Leipzig J, Bushman FD, Taylor GP, Bangham CR.
CONTEXT: However, although
the observed association with integration into transcriptionally active regions
was stronger in vivo than in vitro, there were significantly
fewer integrations into transcription units in vivo (Acembly, RefSeq and
Ensemble gene definitions tested; p = 2.5×10−4, 0.044, 0.0065
respectively) (Table
2). Whereas HTLV-1 proviral integration frequency in transcription units
exceeded expectation in vitro, in vivo there was no deviation from
expected frequencies.
PLoS Pathog. 2008 Mar; 4(3):
e1000027. published online before print March 21, 2008
189- Using native and
syntenically mapped cDNA alignments to improve de novo gene finding.
Stanke M, Diekhans M, Baertsch R, Haussler D.
Bioinformatics. 2008 Mar 1;24(5):637-44. Epub 2008 Jan 24.
188- Multiple
alternative splicing markers for ovarian cancer.
CONTEXT: In this study, we have shown that alternative
splicing patterns can distinguish normal ovary from epithelial
ovarian cancer… The signature identified all normal tissues in a
blinded set of 39 specimens, and 80% of the diverse cancer tissues
regardless of their histologic subtypes. We based our comprehensive
primer design on the AceView database as it has the most
comprehensive EST coverage (34).
In comparison with AceView, only 65% and 45% of our hits were
represented in the smaller, curated, UCSC, and RefSeq databases, respectively.
The fact that the AceView database is near complete for our purposes
was tested by an extensive search through our data for novel
cancer-associated splice events. One possible explanation for the
lack of novel sequences recovered by this query is that we
concentrated on well-known genes. It is possible that novel
cancer-specific splicing events could be discovered in less well
annotated genes.
Cancer Res. 2008 Feb 1;68(3):657-63.
PMID: 18245464
187- Comprehensive analysis of affymetrix exon arrays using BioConductor.
PLoS Comput Biol. 2008 Feb;4(2):e6. No abstract available.
PMID: 18463711
186- Genetic analysis
of chromosome 20-related posterior polymorphous corneal dystrophy: genetic
heterogeneity and exclusion of three candidate genes.
Hosseini SM, Herd S, Vincent AL, Héon E.
CONTEXT: Characterizing VSX1 transcript variants: EST alignments available in the UCSC genome browser and exon predictions based on EST clustering, such as ECgene v1.2 and AceView, provided evidence of novel exons downstream to VSX1. This was confirmed by RT-PCR on human adult retinal RNA using primers in predicted exons that produced PCR products of expected sizes.
Mol Vis. 2008 Jan 16;14:71-80.
PMID: 18253095
185- hsp70 genes in
the human genome: Conservation and differentiation patterns predict a wide
array of overlapping and specialized functions.
Brocchieri L, Conway de Macario E, Macario
AJ.
CONTEXT: many more processed variants for the majority of the genes were predicted from the analysis of EST (Expressed Sequence Tag) and SAGE (Serial Analysis of Gene Expression) data. Prediction of transcript variants based on these data (ECgene database [14,15] and NCBI AceView database, D. Thierry-Mieg, J. Thierry-Mieg, M. Potdevin and M. Sienkiewicz, unpublished) are displayed and compared in Table 4,
BMC Evol Biol. 2008 Jan 23;8:19.
PMID: 18215318
2007 : 35 articles
184- The 3'
untranslated region of human Cyclin-Dependent Kinase 5 Regulatory subunit 1
contains regulatory elements affecting transcript stability.
Moncini S, Bevilacqua A, Venturin M,
Fallini C, Ratti A, Nicolin A, Riva P.
CONTEXT: Given the key role of CDK5R1 in the development, differentiation and physiology of brain and its involvement in extra-neuronal cell activities, it is conceivable that accurate spatio-temporal regulation of its expression is needed. CDK5R1 is characterized by an extended 3'-UTR (2725 bp), which accounts for about 75% of the whole transcript and is among the 5% longest annotated 3'-UTRs [21, according to AceView].
BMC Mol Biol. 2007 Dec 3;8:111.
PMID: 18053171
183- Novel definition files for human GeneChips based on
GeneAnnot.
BMC Bioinformatics. 2007 Nov 15;8:446.
PMID: 18005434 [PubMed - indexed for MEDLINE]
182- Decline of nucleotide excision repair capacity in aging
Caenorhabditis elegans.
Meyer JN, Boyd WA, Azzam GA, Haugen AC, Freedman JH, Van Houten B.
Genome Biol. 2007;8(5):R70.
181- UTRome.org: a platform for 3'UTR biology in C. elegans.
Mangone
M, Macmenamin P, Zegar C, Piano F, Gunsalus K.
CONTEXT: Recent studies indicate that a substantial proportion of characterized transcripts in humans and other species experience alternative splicing of a terminal exon or alternative polyadenlyation (polyA) site usage (10–12). For example, careful curation of mRNA sequence data shows that at least one-third of genes analyzed in human, mouse and Arabidopsis, and over 10% in C. elegans, express transcripts that share a terminal exon but use different polyA signal (PAS) sites, resulting in 3'UTRs of different lengths [(12); D. and J. Thierry-Mieg, personal communication].
Nucleic Acids Res. 2007 Nov 5; [Epub ahead of print]
PMID: 17986455
180 - An adult form of Alexander disease: a novel mutation in glial fibrillary acidic protein.
Ohnari
K, Yamano M, Uozumi T, Hashimoto T, Tsuji S, Nakagawa M.
CONTEXT: The 9 exons in GFAP were sequenced by the cycle sequence method
(ABI PRISM Dye Terminator Cycle Sequencing Kit) with primer sets that were
designed based on the GFAP sequence published in AceView
(http://www.ncbi.nlm.nih.gov/AceView/), then analyzed using an autosequencer
(ABIPRISM310).
J Neurol. 2007 Oct;254(10):1390-1394. Epub 2007 Oct 15.
PMID: 17934883
179- Subcellular
distribution of human RDM1 protein isoforms and their nucleolar accumulation in
response to heat shock and proteotoxic stress.
CONTEXT: evidence for alternative splicing of RDM1 pre-mRNA was also reported in the AceView annotations of the National Center for Biotechnology Information (NCBI) human genome database (http://www.ncbi.nih.gov/IEB/Research/Acembly/index.html). In addition, the database suggested the existence of an alternative translation initiation codon located within intron 1 (position 495 on sequence accession number NC_000017.9) (Figure 1A).
Nucleic Acids Res. 2007;35(19):6571-87. Epub 2007 Sep 28.
PMID: 17905820
178 - A detailed
transcript-level probe annotation reveals alternative splicing based microarray
platform differences.
Lee JC, Stiles D, Lu J, Cam MC.
CONTEXT: Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences.
BMC Genomics. 2007 Aug 20;8(1):284 [Epub ahead of print]
PMID: 17708771
177 - Variation in the gene coding for the M5
Muscarinic receptor (CHRM5) influences cigarette dose but is not associated
with dependence to drugs of addiction: evidence from a prospective population
based cohort study of young adults.
Anney RJ, Lotfi-Miri M, Olsson CA, Reid SC, Hemphill SA, Patton GC.
CONTEXT: The gene structure of CHRM5 was described through AceView, based on Build 35.1 data [21]. [note: There are two promoters in AceView, only one in RefSeq. AceView was used to choose the regions to be tested]. In silico sequence variation detection was performed using the dbSNP repository. Our data suggest that variation within the CHRM5 locus may play an important role in tobacco and cannabis but not alcohol addiction in European ancestry populations. This is the first study to show an association between CHRM5 and substance use in humans.
BMC Genet. 2007; 8: 46. published online before print July 3, 2007
Abstract | Full Text | PDF-267K
176 -
Differing patterns of selection in alternative and constitutive splice sites.
Garg K, Green P.
CONTEXT: Our results illuminate differences between
alternative and constitutive sites and, in particular, strongly support the
idea that alternative sites are under selection to be weak. [AceView was used
for identification and classification of splice sites:]
Note: one more bioinformatics analysis relying on AceView (here
called Acembly) without citing it properly.
Genome Res. 2007 Jul; 17(7): 1015-1022.
175 - Alternative splicing of the FGF
antisense gene: differential subcellular localization in human tissues and
esophageal adenocarcinoma.
Zhang
SC, Barclay C, Alexander LA, Geldenhuys L, Porter GA, Casson AG, Murphy PR.
CONTEXT : [The structure and annotation of the
variants in AceView was used as the startpoint] Organization of the human
FGF-2/FGF-AS gene locus, alternative splicing of FGF-AS/NUDT6 transcripts and
predicted protein products [Fig 1. were extracted from AceView]. a Exons 11 and
13 of the FGF-AS gene are complementary to the 3′ UTR of FGF-2. FGF-AS
splice variants c and d have a common open reading frame and differ only in
their untranslated tails.(…)
J Mol Med.
2007 Nov;85(11):1215-28. Epub 2007 Jun 14.
PMID: 17569023
174 - A new genetic disorder in mitochondrial fatty acid beta-oxidation: ACAD9 deficiency.
He
M, Rutledge SL, Kelly DR, Palmer CA, Murdoch G, Majumder N, Nicholls RD, Pei Z,
Watkins PA, Vockley J.
CONTEXT: [Confirms the existence of alternative exons in AceView] The ACAD9
variant a (GenBank accession numbers CR613592 and
BX415793) (aAugust05 [AceView]) mRNA differs from variant b
(GenBank
accession number NM_014049) (bAugust05 [AceView])
by the presence of an alternative exon 1a at the 5
terminus, one alternative exon 18 resulting from differential
splicing, and four additional exons (19–22) in the 3
UTR (fig.
7a). At least 33 human ESTs containing exon 1a
exist in dbEST.
However, this region is conserved only in primates and
not in other mammals. Alternative exon 1 could be
amplified by PCR from human fibroblast cDNA, substantiating
its existence in vivo (fig.
7b, lane 2).
Am J Hum Genet.
2007 Jul;81(1):87-103. Epub 2007 Jun 4.
PMID: 17564966
173 -
The versatile worm: genetic and genomic resources for Caenorhabditis elegans
research
Igor Antoshechkin, Paul W. Sternberg
SUMMARY: The popularity of Caenorhabditis elegans as a model organism is paralleled by the range of resources that are available to worm researchers. This Review provides a guide to existing C. elegans re
CONTEXT: .....................http://www.wormbase.org WormGenes.........................http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm RNAiDB.............................http://www.rnai.org PhenoB...
Nature Reviews Genetics 8, 518 - 532 (05 Jun 2007) Review
Abstract | Full Text | PDF | Rights and permissions
172 - Chitinase family GH18: evolutionary insights from the genomic history of
a diverse protein family.
CONTEXT: A search of the C. elegans database at the NCBI and other resources such as Wormbase [34] and ACEView [35] identified 37 genes or predicted genes encoding chitinases and related GH18 family members
BMC Evol Biol. 2007 Jun 26;7:96.
PMID: 17594485
171 - The novel neuronal ceroid lipofuscinosis gene MFSD8 encodes a putative lysosomal transporter.
Siintola
E, Topcu M, Aula N, Lohi H, Minassian BA, Paterson AD, Liu XQ, Wilson C,
Lahtinen U, Anttonen AK, Lehesjoki AE.
We identified six different
mutations in the MFSD8 gene (previously denoted "MGC33302"),
which encodes a novel polytopic 518–amino acid membrane
protein …expressed ubiquitously, with several alternatively spliced
variants.
CONTEXT:
[AceView has 1o variants, RefSeq has 1. The existence of the AceView variants
was confirmed experimentally] Both northern-blot and EST database
analyses support the ubiquitous expression of the main MFSD8
transcript, including exons 1–13, whereas the alternatively
spliced variants seem to have more-limited tissue distribution
(NCBI
AceView). In particular, four alternative, partial variants
were present in EST databases (…) The variant lacking both
exons 7 and 8 produces a transcript with an in-frame
deletion of 67 aa, whereas the others lead to frameshifts
and premature stop codons. We verified these and
identified several other alternatively spliced transcripts by RT-PCR
analyses..
Am J Hum Genet. 2007
Jul;81(1):136-46. Epub 2007 May 14.
PMID: 17564970
170 - A novel
missense mutation in the NDP gene in a child with Norrie disease and severe
neurological involvement including infantile spasms.
Lev
D, Weigl Y, Hasan M, Gak E, Davidovich M, Vinkler C, Leshinsky-Silver E,
Lerman-Sagie T, Watemberg N.
CONTEXT: Mutation analysis of the ND gene (NDP) of the affected child
and his mother revealed a novel missense mutation at position c.134T > A
resulting in amino acid change at codon V45E. Electronic database information: 
www.ncbi.nlm.nih.gov/IEB/Research/Acembly
www.ncbi.nlm.nih.gov/Unigene/ESTProfileViewer
Am J Med Genet A. 2007 May 1;143(9):921-4.
PMID: 17334993 [PubMed - indexed for MEDLINE]
169 - DTNBP1
(Dystrobrevin binding protein 1) and schizophrenia: association evidence in the
3' end of the gene.
Duan
J, Martinez M, Sanders AR, Hou C, Burrell GJ, Krasner AJ, Schwartz DB, Gejman
PV.
CONTEXT: [AceView helps identify regions to be tested for genetic association]
... but no mutations in the coding sequences; these
11 SNPs were not associated (nominal p 1 0.05) with schizophrenia in 552 cases
and 552 controls. When all 15 alternatively spliced mRNA transcripts from
AceView (www.ncbi.nlm.nih.gov/IEB/Research/Acembly/; update November 2004) are
considered ( fig. 1 ), 7 missense SNPs can be defined from a total of 10 coding
SNPs available in a search of dbSNP (www.ncbi.nlm.nih.gov/projects/SNP/; build
123) and the literature ( table 2 ). None of these coding variants have so far
been tested in previous association studies. We present here a family based
association study of
Hum Hered. 2007;64(2):97-106. Epub 2007 May
2.
PMID: 17476109
168 - Decline of
nucleotide excision repair capacity in aging Caenorhabditis elegans.
Meyer JN, Boyd
WA, Azzam GA, Haugen AC, Freedman JH, Van Houten B.
CONTEXT: We developed
primers and optimized PCR conditions to adapt our QPCR methodology…Different
nuclear targets were chosen to include genes that we expected to be transcribed
at negligible, medium, or high levels in glp-1 adults, based initially
on available expression data including the Kohara cDNA library [89,
AceView], the Kohara in situ hybridization database
Genome Biol\. 2007; 8(5): R70. published online before print May 1, 2007
PMID: 17472752
Abstract
| Full
Text | PDF-0.7M
| Supplementary
Material |
167 - Expression of multiple catechol-o-methyltransferase
(COMT) mRNA variants in human brain.
Tunbridge EM, Lane TA, Harrison PJ.
CONTEXT: specific primers were designed to sequences in the NCBI Aceview database. Several of the variants alter the predicted coding sequence. Three of these variants correspond to sequences within the Aceview database and could be reliably amplified, while the remaining four do not correspond to any expressed sequence tags and were amplified only once.
Note: we are happy to see good confirmation of the
AceView/GenBank/dbEST/Trace derived transcripts.
Am J Med Genet B Neuropsychiatr
Genet. 2007 May 3; [Epub ahead of print]
PMID: 17477346
166 - Identification and characterization
of the TRIP8 and REEP3 genes on chromosome 10q21.3 as novel candidate genes for
autism
Dries Castermans,
Joris R Vermeesch, Jean-Pierre Fryns, Jean G Steyaert, Wim J M Van de Ven, John
W M Creemers, Koen Devriendt
SUMMARY: Autism is a genetic neurodevelopmental disorder of unknown cause and pathogenesis. The identification of genes involved in autism is expected to increase our understanding … The distal breakpoint disrupts the TRIP8 gene, (…) the same breakpoint abolishes expression of a nearby gene, REEP3, through a position effect. These observations suggest that TRIP8 and REEP3 are both positional candidate genes for autism.
CONTEXT: Although the unreported G/A SNP was located in the
mRNA BC018658, and the UCSC database shows the non-overlapping mRNA BC068557
1200 bp upstream chromosome 10 as the full-length cDNA sequence of REEP3,
we showed that both mRNAs correspond to a single gene. (…) Interestingly, the
transcript was also found on the AceView database [Which had the correct
extension of more than 2 kb of the 3’UTR relative to the RefSeq, and contained
the observed polymorphism.]
European Journal of Human Genetics 15, 422 - 431 (01 Apr 2007) Article
Abstract | Full Text | PDF | Rights and permissions |
165 - Association analysis of the
chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia
A Christoforou, S Le Hellard, P A Thomson, S W Morris, A Tenesa, B S Pickard, N R Wray, W J Muir, D H Blackwood, D J Porteous, K L Evans
SUMMARY: Several independent linkage studies have identified chromosome 4p15?p16 as a putative region of susceptibility for bipolar disorder (BP), schizophrenia (SCZ) and related phenotypes. Prev
CONTEXT: ...from the NCBI mRNA reference sequence collection and (iii) main prediction class AceView genes that do not correspond to Known or RefSeq genes. AceView genes are constructed from mRNA, expressed sequence tag (EST) and genomic... [Note: of 4 regions where SNPs associated to the diseases were found, three were annotated as genes in AceView and not known in other databases].
Molecular Psychiatry 12, 1011 - 1025 (24 Apr 2007) Original Article
Abstract | Full Text | PDF | Rights and permissions |
164 - Bioinformatics for Geneticists (Second Edition)
Editor(s): Michael R. Barnes
CONTEXT: talks about Acembly program, 71, 77 and Acembly structure prediction program, 71, 77
Published Online: 21 Mar 2007
Print ISBN: 9780470026199 Online ISBN: 9780470059180
Copyright © 2007 John Wiley & Sons, Ltd
163 - Primary function analysis of human mental retardation related gene CRBN.
Xin
W, Xiaohua N, Peilin C, Xin C, Yaqiong S, Qihan W.
CONTEXT:
Each part of the insert was sequenced at least three times bi-directionally.
Subsequent editing and assembly of all the sequences from one clone was
performed using Acembly (Sanger’s Center).
Mol Biol Rep. 2007 Mar 23; [Epub
ahead of print]
PMID: 17380424
162 - Thematic review
series: Adipocyte Biology. Lipodystrophies: windows on adipose biology and
metabolism.
Hegele RA, Joy TR, Al-Attar SA, Rutt BK.
CONTEXT: Two recently described FPLD2 mutations, LMNA
D230N and R399C, occur upstream of the lamin A NLS (...).
Reannotation of sequences of previously studied genes can identify
new sequences to be screened, leading to the discovery of new
mutations (42).
In this regard, a recent version of the
J Lipid Res. 2007
Jul;48(7):1433-44. Epub 2007 Mar 20. Review.
PMID: 17374881
161 - The
identification and characterization of a novel protein, c19orf10, in the
synovium.
Weiler T, Du Q, Krokhin O, Ens W, Standing K, El-Gabalawy H, Wilkins JA.
CONTEXT: A competitive enzyme-linked immunosorbent assay confirmed the presence of microgram levels of c19orf10 in the synovial fluids of patients with one of various arthropathies. Collectively, these results suggest that c19orf10 is an FLS-derived protein that is secreted into the synovial fluid.
The c19orf10 gene is located on chromosome 19p13.3 and spans approximately 30 kbp [15, AceView web site] (Figure 2). A survey of the available cDNA clones suggests the possibility of three splice variants for c19orf10 [16] (Figure 2b). All of the c19orf10 peptides identified by our analysis are present in the c19orf10.b sequence (highlighted peptides, Figure 2c).
Arthritis Res Ther. 2007; 9(2): R30. published online before print March 15, 2007
Abstract
| Full
Text | PDF-1.3M
|
160 -
Transcript-based redefinition of grouped oligonucleotide probe sets using
AceView: high-resolution annotation for microarrays.
Lu J, Lee JC, Salit ML, Cam MC.
CONTEXT: Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes….We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design.
BMC Bioinformatics. 2007 Mar 29;8:108.
159 - Clusterin expression in normal mucosa and colorectal cancer.
Andersen
CL, Schepeler T, Thorsen K, Birkenkamp-Demtroder K, Mansilla F, Aaltonen LA,
Laurberg S, Orntoft TF.
CONTEXT: To identify novel CLU variants, we inspected the CLU entries in
various alternative splicing databases (The AceView Genes, www.ncbi.nlm.nih.gov/IEB/Research/Acembly;
the Alternative Splicing Annotation Project (ASAP)
Mol Cell Proteomics.
2007 Jun;6(6):1039-48. Epub 2007 Feb 23.
PMID: 17322305
158 - Localizing hotspots of antisense transcription.
Finocchiaro G, Carro MS, Francois S,
Parise P, DiNinni V, Muller H.
CONTEXT: Antisense transcripts were identified according to the criteria
defined by (11).
In order to minimize the number of false positives, only antisense ESTs which
are supported by an Aceview gene model were considered. Antisense transcription
and bidirectional gene pairs. (A) Fraction of head-to-head and
antisense Aceview gene models. (B) Distribution of distances
between the 5′end of Aceview gene models and the 5′end of the
RefSeq transcripts. Only Aceview gene models whose 5′end is located within
5
kb
of the RefSeq transcription start are shown (4270).
Nucleic Acids Res. 2007;35(5):1488-500. Epub 2007 Feb 6.
157 - Novel LMNA
mutations seen in patients with familial partial lipodystrophy subtype 2
(FPLD2; MIM 151660).
Lanktree
M, Cao H, Rabkin S, Hanna A, Hegele R.
CONTEXT: Re-annotation of the sequences of previously studied genes can
identify new sequences that can be screened, leading to the discovery of new
mutations (14). In this regard, the
recent release of NCBI AceView (31 August, 2006), which annotates human genes
by aligning cDNA and expressed sequence tags, indicates that LMNA may be
much more variable at the transcriptional level than had been previously
thought, with perhaps >40 exons and >10 distinct mRNA transcripts (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly).
This evolving sequence annotation for LMNA might lead to the
identification of new mutations.
Note: we hope that AceView will have such a positive impact on helping discover new allele-to-disease associations!
Clin Genet. 2007 Feb;71(2):183-6.
156 - Cystatin B: mutation detection, alternative splicing and expression in progressive myclonus epilepsy of Unverricht-Lundborg type (EPM1) patients
Tarja Joensuu, Mervi Kuronen, Kirsi Alakurtti, Saara Tegelberg, Paula Hakala, Antti Aalto, Laura Huopaniemi, Nina Aula, Roberto Michellucci, Kai Eriksson, Anna-Elina Lehesjoki
SUMMARY: Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) is an autosomal recessive neurodegenerative disorder caused by mutations in the cystatin B gene (CSTB) that encodes
CONTEXT: ...I and II (Clontech) and sequenced. Two variant transcripts were identified from EST sequences present in ASAP or AceView databases in NCBI, while two were identified by RT-PCR. The complete coding region of mouse Cstb2 was amplified...
European Journal of Human Genetics 15, 185 - 193 (01 Feb 2007) Article
Abstract | Full Text | PDF | Rights and permissions
155 - Identification
and characterization of the TRIP8 and REEP3 genes on chromosome 10q21.3 as
novel candidate genes for autism
Dries Castermans,
Joris R Vermeesch, Jean-Pierre Fryns, Jean G Steyaert, Wim J M Van de Ven, John
W M Creemers, Koen Devriendt
CONTEXT: we were able to amplify a cDNA fragment of the expected size of 1.6 kb, which had the predicted nucleotide sequence, identical to that of the corresponding fragment of the IMAGE562868 clone (data not shown). Interestingly, the transcript was also found on the AceView database, referred to as TB2_DP1_HVA22.4b. In conclusion, the full-length REEP3 gene (NM_001001330) consists of eight...
European Journal of Human Genetics (07 Feb 2007) Article
Abstract | Full Text | PDF | Rights and permissions |
154 - Mapping of transcription
start sites of human retina expressed genes.
Roni V, Carpio R,
Wissinger B.
CONTEXT: In silico analysis: …considering also gene prediction (GENSCAN, implemented in the UCSC Genome Browser) and gene annotation that are confirm by at least one EST [43 AceView].
BMC Genomics. 2007; 8: 42. published online before print February 7, 2007
Abstract | Full Text | PDF-0.6M | Supplementary Material |
153 - C6ORF32 is
upregulated during muscle cell differentiation and induces the formation of
cellular filopodia.
Yoon S, Molloy MJ, Wu MP, Cowan DB, Gussoni E.
CONTEXT: Expression of multiple C6ORF32 isoforms in human fetal myoblasts:
C6orf32 is an open reading frame putatively encoding 12 alternatively spliced forms (NCBI, AceView). To analyze whether multiple isoforms of this protein are expressed in human fetal muscle cells under differentiation in vitro, western blot analysis was performed (Figure 3A). Several isoforms of C6ORF32 protein were detected in human fetal muscle cells during fusion, and the amount of some of these isoforms increased during differentiation (Figure 3A, black arrowheads).
Two known alternatively spliced forms of c6orf32 were amplified by RT-PCR from human fetal muscle cells (Iso 1 and Iso 2). Primers were designed according to the nucleotide sequences of AB002384 (1068 aa), which encodes the longest known isoform, and NM_015864 (Iso 2, 591 aa). As shown in Figure 3A, Iso 1 (1018 aa), an isoform known to be expressed in brain (NCBI, AceView), and Iso 2 are expressed during differentiation of human fetal primary myoblasts. C6ORF32 Iso 2 (591 aa) is also present in muscle and is 50 amino acids longer at its N-terminus than PL48, which is expressed in placenta (Figure 3B) (Dakour et al., 1997).
Dev Biol. Author manuscript; available in PMC 2007 January
22.
| Abstract
| Full
Text | PDF-3.9M
|
152 - Modern origin of numerous alternatively spliced human introns from tandem arrays.
Zhuo
D, Madden R, Elela SA, Chabot B.
CONTEXT: This work was an explicit collaboration
between this group and us at AceView, yet we were surprised to discover the
article in print. AceView was their main source and to our knowledge, they
relied on us for annotation of fuzzy and other non-validated introns, unlike
what they say in their methods section: “The
NCBI and AceView data sets were first systematically checked to minimize
errors. ‘‘Fuzzy’’ introns, misalignment of exons/introns, and data errors (in
AceView) were removed after careful visual inspection and sequence comparisons.
Only GT-AG, GC-AG, and AT-AC introns were used. The final NCBI and AceView data
sets contained 183,774 and 304,008 introns, respectively.” Their cleaning of data errors consisted in
taking for granted our quality annotations, which we sent them and taking them
on their account. They received personally the data, instructions, and the news
letter, which is public on our web site. If they found errors in AceView, they
certainly did not submit them to us. These people do not deserve to be called
scientists.
The
4.5 million cDNA sequences aligned on the genome define 312,932 different
standard introns, all well supported (i.e. a cDNA sequence exactly matches the
genome over 16 bp, equally split on both sides of the intron boundary).
97.7% are gt-ag, 2.2% gc-ag (a bit high?) and 0.08% at-ac (265 cases). An
additional 4485 introns are anomalous, and most probably correspond to defects
in the cDNA clones (or the genome). (…)
Using
this simple measure of standard intron counts, we may ask what is the added
value of each type of data:
-
The NM and NR RefSeqs see a total of 171,864 standard introns (and 442
non-standard), or 55% of the total number of introns in the human cDNAs from
the public databases. Therefore, despite the small size of the RefSeq database,
they already touch more than half of the known standard introns. Their pattern
is: 99.07% gt-ag, 0.80% gc-ag, 0.11% U12 at-ac (182 cases).
-
If we considered only the 174,129 GenBank mRNAs, they define a total of
226,014 standard introns, 72% of the total (98.7% gt-ag, 1.17% gc-ag, 0.10%
at-ac (228 cases); in addition to 1623 non-standard introns). “
Proc
Natl Acad Sci U S A. 2007 Jan 16;104(3):882-6. Epub 2007 Jan 8.
PMID: 17210920 [PubMed - indexed for MEDLINE]
151 - Serotonin
Transporter mRNA Levels are Associated With the Methylation of an Upstream CpG
Island.
Philibert R, Madan A, Andersen A, Cadoret R, Packer H, Sandhu H.
CONTEXT: The existence, location, size, and sequence of the CpG island were identified using the default browser settings of the University of California Genome Browser (UCSC) website. The existence of the alternative splicing form of 5HTT was also determined using the default AceView settings of the browser.
We describe a CpG island in the 5
region
of the 5HTT gene that contains an alternative exon 1 and possible
promoter for 5HTT. We then confirm the existence of this transcript and
ascertain the methylation status of this CpG island in 49 lymphoblast cell
lines. We demonstrate that methylation at this CpG island is associated with
decreased levels of 5HTT.
Am J Med Genet B Neuropsychiatr Genet. 2007 Jan 5;144(1):101-5.
150 - Cloning and characterization of a gene encoding the human putative ubiquitin conjugating enzyme E2Z (UBE2Z).
Gu
X, Zhao F, Zheng M, Fei X, Chen X, Huang S, Xie Y, Mao Y.
CONTEXT: Each part of the insert was sequenced at least three times
bidirectionally. Subsequent editing and assembly of all the sequences from one
clone was performed using Acembly (Sanger’s Center). [These authors do not know
that Acembly is CNRS,
Mol Biol Rep. 2007
Sep;34(3):183-8. Epub 2006 Dec 12.
PMID: 17160626
41 in 2006
149- Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S.
ECgene: an alternative splicing
database update.
Nucleic
Acids Res. 2007 Jan;35(Database
issue):D99-103. Epub 2006 Nov 28.
148- Leukemia-associated
antigenic isoforms induce a specific immune response in children with T-ALL.
Dohnal AM, Inthal A, Felzmann T, Glatt S, Sommergruber W, Mann G, Gadner H, Panzer-Grumayer ER.
CONTEXT: Sequences were further analyzed for homology with
known genes using public databases (BLAT, BLAST, SEREX), exon usage (AceView/
NCBI database) and functional domains (
Int J Cancer. 2006 Dec 15;119(12):2870-7.
147 - ECgene: an alternative splicing database update.
Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S.
CONTEXT: AceView provides a
comprehensive overview of functional and structural aspects of alternatively
spliced genes for human, worm and Arabidopsis genomes (10)….
ASviewer extends the features of ECfunction to support other gene models
including RefSeq, Ensembl and AceView. The transcript models can be readily
compared using the detailed information for exons and introns available in the
baloon help.
Nucleic Acids Res. 2006; published online before print November 28, 2006
Abstract
| Full
Text | PDF-208K
|
146 - Identification
of the Slynar Gene (AY070435) and Related Brain Expressed Sequences as a
Candidate Gene for Susceptibility to Affective Disorders Through Allelic and
Haplotypic Association With Bipolar Disorder on Chromosome 12q24.
Kalsi
G, McQuillin A, Degn B, Lundorf MD, Bass NJ, Lawrence J, Choudhury K, Puri V,
Nyegaard M, Curtis D, Mors O, Kruse T, Kerwin S, Gurling H.
CONTEXT: The most promising candidate gene in the region
implicated by us is denoted Slynar in the ACEVIEW database
(http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly ... ACEVIEW-generated
gene names are the accepted names for genes that have not yet been well
characterized. The region is not well characterized in terms of ... Note: Slynar is the temporary AceView name;
it will hopefully get a Hugo name.
Am J
Psychiatry. 2006 Oct;163(10):1767-1776.
145 - Transmission disequilibrium test provides evidence of
association between promoter polymorphisms in 22q11 gene DGCR14 and
schizophrenia.
Wang
H, Duan S, Du J, Li X, Xu Y, Zhang Z, Wang Y, Huang G, Feng G, He L.
CONTEXT: The human DGCR14 gene was first identified and cloned by Rizzu and his colleagues in 1996 (Rizzu et al., 1996), and it is thought to be essential for early embryonic development (Lindsay et al., 1998). The descriptions in AceView (www.ncbi.nih.gov/IEB/Research/Acembly) suggest the DGCR14 gene is highly expressed, about 3.9 times the average..
J Neural Transm. 2006 Oct;113(10):1551-61. Epub 2006 Jan 25.
144 - Gene Array
Profiles of Alcohol and Aldehyde Metabolizing Enzymes in Brains of C57BL/6 and
DBA/2 Mice.
Bhave
SV, Hoffman PL, Lassen N, Vasiliou V, Saba L, Deitrich RA, Tabakoff B.
CONTEXT: A nucleotide database search (AceView database, http://www.ncbi.nih.gov/IEB/Research/Acembly),
for splice variants revealed the presence of at least 7 alternatively spliced
variants of ALDH9A1 in humans. The presence of such splice variants in mice has
not been previously reported, but could explain differences in the detection of
differential expression of the given transcript by the probes on the 2
platforms.
Alcohol Clin Exp Res. 2006 Oct;30(10):1659-69.
143 - snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.
Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH.
CONTEXT: Selecting candidates using locateGenome program.
With the exception of U3, mgU2-25/61, mgU12-22/U4-8, mgU12 and U13, all snoRNAs
are located in introns of spliced mRNAs. We investigated the size distribution
of all known snoRNA-hosted introns… The locateGenome program first locates the
candidates according to the UCSC AceView gene data of human genomic coordinates
and orientations which includes >250
000
alt-splicings. The program then selects C/D candidates which are located within
introns <50 000 bp and H/ACA candidates which are located within introns
<110000
bp.
Nucleic
Acids Res. 2006 Oct; 34(18): 5112-5123. published
online before print September 20, 2006
Abstract | Full Text | PDF-0.9M | Supplementary Material |
142 - Human
Lineage–Specific Amplification, Selection, and Neuronal Expression of DUF1220
Domains
Magdalena C. Popesco, Erik J. MacLaren, Janet Hopkins, Laura Dumas, Michael Cox, Lynne Meltesen, Loris McGavran, Gerald J. Wyckoff, and James M. Sikela
CONTEXT:......It has been estimated that 34 different human
genes encode DUF1220 domains (table S3) ( www.ncbi.nlm.nih.gov/IEB/Research/Acembly
). Pfam (Version 17.0) ( 9 ) predicts that 60 human DUF1220-containing proteins
exist, containing a total of 271 DUF1220 domains......
Science 1 September 2006 313: 1304-1307 [DOI: 10.1126/science.1127980]
(in Reports)
Abstract » Full Text » PDF » Supporting Online Material »
141 - U1-like snRNAs lacking complementarity to canonical 5’ splice sites.
Kyriakopoulou C, Larsson P, Liu L, Schuster J, Sóderbom F, A. Kirsebom L, Virtanen A.
CONTEXT: To investigate if the variant U1A snRNAs could act on noncanonical 5′SSs, we searched the human AceView database for noncanonical 5′SS sequences that could be recognized by U1A5, U1A6, or U1A7 snRNA through formation of six or more base pairs, including base-pair interactions with the noncanonical dinucleotide at the 5′SS. We found 301 (CU dinucleotide; U1A5 snRNA), 344 (249 AA dinucleotide and 95 GA dinucleotide; U1A6 snRNA), and 16 (UU dinucleotide; U1A7 snRNA) noncanonical 5′SS sequences that fulfilled this criteria (Supplemental Table S2).
RNA. 2006 Sep; 12(9): 1603-1611
Abstract | Full Text | PDF-0.7M |
140 - Detection of autoantibodies to the BTB-kelch protein KLHL7 in cancer sera.
Bredholt G, Storstein A, Haugen M,
Krossnes BK, Husebye E, Knappskog P, Vedeler CA.
CONTEXT: According to the NCBI database AceView (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly),
the KLHL7 gene produces 15 protein-coding splice variants ranging from 336 to
3264 bp encoding 14 putative protein..
Scand J Immunol. 2006 Sep;64(3):325-35.
139 - Cystatin B: mutation detection, alternative splicing and expression in progressive myclonus epilepsy of Unverricht-Lundborg type (EPM1) patients
Tarja Joensuu, Mervi Kuronen, Kirsi Alakurtti, Saara Tegelberg, Paula Hakala, Antti Aalto, Laura Huopaniemi, Nina Aula, Roberto Michellucci, Kai Eriksson, Anna-Elina Lehesjoki
CONTEXT: ...I and II (Clontech) and sequenced. Two variant transcripts were identified from EST sequences present in ASAP or AceView databases in NCBI, while two were identified by RT-PCR. The complete coding region of mouse Cstb2 was amplified...
European Journal of Human Genetics (27 Sep 2006) Article
138 - An RNA gene
expressed during cortical development evolved rapidly in humans.
CONTEXT: We found that an automated cDNA analysis computer program, Acembly (http://www.aceview.org) had predicted a 58 amino acid in the human HAR1F transcript and named it “rerty”.
Note: this gene was well defined in AceView at the transcript level since 2001 and the authors knew it, but for some reason were shy about citing AceView.
Nature. 2006 Sep 14;443(7108):167-72. Epub 2006 Aug 16.
137 - Why do
mutations in the ubiquitously expressed housekeeping gene IMPDH1 cause
retina-specific photoreceptor degeneration?
Bowne SJ, Liu Q, Sullivan LS, Zhu J, Spellicy CJ, Rickman CB, Pierce EA, Daiger SP.
SUMMARY: The predominant transcripts of IMPDH1 in human retina are the result of alternate splicing and alternate start sites of translation. They are significantly different from those in other tissues, and these variant transcripts encode distinct proteins. Further, the proportions of IMPDH1 transcripts and proteins in human retina are different from those in mouse retina. Identification of unique retinal isoforms supports the existence of a novel IMPDH1 function in the retina, one that is probably altered by disease-causing mutations.
CONTEXT: The presence of exon 13b, a 17-bp exon located in
the genomic sequence between exons 13 and 14, was also seen in the ACEview
database, but was only present in two of the 162 human cDNA clones,
both of which were from retinal libraries.... search within the ACEview
database (http://ncbi.nlm.nih.gov/IEB/Research/Acembly; provided in
the public domain by NCBI) indicated that splicing of exon A to exon
1 was common in a range of tissues, including retina. Splicing from
exons A to 1 creates an in-frame, alternate methionine in exon A.
Invest Ophthalmol
136 - The MicroArray Quality Control (MAQC) project
shows inter- and intraplatform reproducibility of gene expression measurements
Leming Shi, Laura H Reid, Wendell D Jones, Richard Shippy, Janet A Warrington, Shawn C Baker, Patrick J Collins, Francoise de Longueville, Ernest S Kawasaki…
CONTEXT: ...and Supplementary Notes online) to the RefSeq human mRNA database (http://www.ncbi.nlm.nih.gov/RefSeq) and to the AceView database (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly), a less curated but more comprehensive database,...
Nature Biotechnology 24, 1151 - 1161 (01 Sep 2006) Research
135 - Large-scale
identification and characterization of alternative splicing variants of human
gene transcripts using 56 419 completely sequenced and manually annotated
full-length cDNAs.
Takeda JI, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T.
Nucleic Acids Res. 2006; 34(14): 3917-3928. published online before print August 12, 2006
Abstract | Full Text | PDF-464K |
134 - The metastasis
suppressor, Ndrg-1: a new ally in the fight against cancer.
Kovacevic
Z, Richardson DR.
CONTEXT: …Studies
examining the protein structure of Ndrg-1 have revealed interesting
characteristics. The AceView database from NCBI indicates that Ndrg-1 and other
NDRG family members have an α/β hydrolase-fold motif, which is
commonly found in hydrolytic enzymes
Carcinogenesis. 2006 Aug 18; [Epub ahead of print]
133 - Convergent
evidence that oligodendrocyte lineage transcription factor 2 (OLIG2) and
interacting genes influence susceptibility to schizophrenia.
CONTEXT: Probe set ERBB4
214053_at matches an ERBB4 transcript that has an
extended 3' UTR (ACEview transcript ERBB4.aAug05) relative
to the reference sequence…the data differ between different probe sets of ERBB4
is not surprising, because ERBB4 has multiple transcripts…
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12469-74. Epub 2006 Aug 4.
132 - AceView: a comprehensive cDNA-supported gene and transcripts annotation
Thierry-Mieg
D, Thierry-Mieg J
Genome Biology 2006, 7(Suppl 1):S12
(7 August 2006)
131 - EGASP: the human
ENCODE Genome Annotation Assessment Project
Guigó R,
Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner
M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J,
Hubbard T, Lewis SE, Reese MG
CONTEXT: For the mRNA evaluation, ACEVIEW reached
88% sensitivity at 79% specificity, ... ACEVIEW was the most
sensitive prediction method for all exons (coding and ...
Genome Biology 2006, 7(Suppl 1):S2
(7 August 2006)
130 - GENCODE: producing a
reference annotation for ENCODE.
Harrow
J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG,
Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.
CONTEXT: Almost all the predictors (with AceView the notable exception) under-predict coding (and non-coding) splice variants, most predicting one transcript per gene.
Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.
129- Pairagon+N-SCAN_EST: a model-based gene annotation pipeline
Arumugam
M, Wei C, Brown RH, Brent MR
CONTEXT: Among the
methods that use mRNA / EST evidence , AceView identifies the two
introns and ENSEMBL identifies one of them . There are also two AT - AG introns
... All other programs except AceView do not predict anything in that
locus. N-SCAN_EST missed an exon even though there is EST evidence for it. We
believe that lack of conservation overwhelmed the EST evidence for that exon.
Genome Biology 2006, 7(Suppl 1):S5
(7 August 2006)
128 - Analysis of a
new homozygous deletion in the tumor suppressor region at 3p12.3 reveals two
novel intronic noncoding RNA genes.
Angeloni
D, ter Elst A, Wei MH, van der Veen AY, Braga EA, Klimov EA, Timmer T,
Korobeinikova L, Lerman MI, Buys CH.
CONTEXT: Acembly annotated the gene as a single exon transcript of 3.1 kb. Interestingly, the align- ... Acembly annotated this transcript as a puta- ... The discovery of two EST clusters within the deleted region led to the isolation of two noncoding RNA (ncRNA) genes. These were subsequently found differentially expressed in various tumors when compared to their normal tissues. The ncRNA and other highly conserved sequence elements in the deleted region may represent miRNA targets of importance in cancer initiation or progression.
Genes Chromosomes Cancer. 2006 Jul;45(7):676-91.
127 - SEL1L a
multifaceted protein playing a role in tumor progression.
Biunno I, Cattaneo M, Orlandi R, Canton C,
Biagiotti L, Ferrero S, Barberis M, Pupa SM, Scarpa A, Menard S.
SUMMARY: …SEL1L has a very complex structure made up of modules: genomically it consists of 21 exons featuring several alternative transcripts encoding for putative protein isoforms. This structural complexity ensures protein flexibility and specificity, indeed the protein was found in different sub-cellular compartments and may turn on a particular transcript in response to specific stimuli. The overall architecture of SEL1L guarantees an exquisite regulation in the expression of the gene.
CONTEXT: Aceview
program (August 2005) (http://www.ncbi.nlm.nih.gov/AceView) supports the presence of
splice variants and predicts at least four different transcripts putatively
encoding for four protein isoforms (Fig. 2A,B)
and five…splicing events that occur within the ninth and eighth exons,
respectively, differing dramatically in the extent of their 3terminal
ends and in the transcription initiation start sites. These were experimentally
detected using specific primers by RT-PCR analysis (Cattaneo et al., personal
observations). (all the analysis is based an AceView and corroborates all the
transcripts and the annotations)
J Cell Physiol. 2006 Jul;208(1):23-38. Review.
126- Mutations in GLIS3 are responsible for a rare syndrome with neonatal diabetes mellitus and congenital hypothyroidism
Valérie Senée, Claude Chelala, Sabine Duchatelet, Daorong Feng, Hervé Blanc, Jack-Christophe Cossec, CÉline Charon, Marc Nicolino, Pascal Boileau, Douglas R Cavener, Pierre Bougnères, Doris Taha, CÉcile Julier
SUMMARY: We recently described a new neonatal diabetes syndrome associated with congenital hypothyroidism, congenital glaucoma, hepatic fibrosis and polycystic kidneys. Here, we show that this
CONTEXT: ...transporter (SLC1A1) and part of the 5' UTR of the gene encoding GLI similar 3 (GLIS3), as predicted by NCBI AceView. Affected individuals in NDH3 carried a homozygous 149-kb deletion that overlapped only a portion of the 5' UTR... We used primers located in all exons referenced in AceView or located in referenced ...
Nature Genetics 38, 682 - 687 (01 Jun 2006) Letters
125- microRNA target predictions in animals
Nikolaus Rajewsky
CONTEXT: ...more detailed 3' UTR annotations in the future (see, for example, Aceview (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly)). Almost all algorithms used evolutionary conservation of target sites as a filter for biologically...
: ...part of possibly varying length. In two independent ongoing analyses (J. Thierry-Mieg and D. Thierry-Mieg, Aceview, personal communication; and W. Majoros and U. Ohler, personal communication), roughly 70% and 40%, respectively, of...
Nature Genetics 38, S8 - S13 (01 Jun 2006) Perspective
124- Mutations in
GLIS3 are responsible for a rare syndrome with neonatal diabetes mellitus and
congenital hypothyroidism
Valérie Senée, Claude Chelala, Sabine Duchatelet, Daorong Feng, Hervé Blanc, Jack-Christophe Cossec, Céline Charon, Marc Nicolino, Pascal Boileau, Douglas R Cavener, Pierre Bougnères, Doris Taha, Cécile Julier
CONTEXT: [AceView correctly predicted an alternative variant and was instrumental in defining the polymorphism as part of the gene. Great work that team did!] The affected individual in NDH2 carried a homozygous 426-kb deletion, which encompasses the gene encoding the neuronal/epithelial high-affinity glutamate transporter (SLC1A1) and part of the 5' UTR of the gene encoding GLI similar 3 (GLIS3), as predicted by NCBI AceView. Affected individuals in NDH3 carried a homozygous 149-kb deletion that... URLs. NCBI AceView: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/.
Nature Genetics 38, 682 - 687 (01 Jun 2006) Letters
123- A Novel MGST2 Non-Synonymous Mutation in a Chinese
Pedigree with Psoriasis Vulgaris
Kai-Lin Yan, Xue-Jun Zhang, Zhi-Min Wang, Sen Yang, Guo-Long Zhang, Jian Wang, Feng-Li Xiao, Min Gao, Yong Cui, Jian-Jun Chen, Xing Fan, Liang-dan Sun, Qing Xia, Kai-Yue Zhang, Zhen-min Niu, Shi-Jie Xu, Andreas Tzschach, Hilger Ropers, Wei Huang, Jian-Jun Liu
CONTEXT: ...of MGST2, there are 11 additional putative coding exons within the MGST2 region (http://www.ncbi.nlm.nih.gov/AceView/ ). We sequenced all the 16 known and suggested exons, exon–intron boundaries and approximately 2,000 bp of 5'...
Journal of Investigative Dermatology 126, 1003 - 1005 (01 May 2006) Original Article
122- The PANE1 gene
encodes a novel human minor histocompatibility antigen that is selectively
expressed in B-lymphoid cells and B-CLL.
SUMMARY: an alternative transcript of the
proliferation-associated nuclear element 1 (PANE1) gene
encodes a novel human leukocyte antigen (HLA)-A*0301-restricted
mHAg that is selectively expressed in B-lymphoid cells. The
antigenic peptide is entirely encoded within a unique exon not
present in other PANE1 transcripts. Sequencing of PANE1
alleles in mHAg-positive and mHAg-negative cells demonstrates that
differential T-cell recognition is due to a single nucleotide
polymorphism within the variant exon that replaces an arginine codon
with a translation termination codon. The PANE1 transcript
that encodes the mHAg is expressed at high levels in resting CD19+
B cells and B-lineage chronic lymphocytic leukemia (B-CLL) cells,
and at significantly lower levels in activated B cells. Activation
of B-CLL cells through CD40 ligand (CD40L) stimulation decreases
expression of the mHAg-encoding PANE1 transcript and
reciprocally increases expression of PANE1 transcripts
lacking the mHAg-encoding exon. These studies suggest distinct roles
for different PANE1 isoforms in resting compared with activated CD19+
cells, and identify PANE1 as a potential
therapeutic target in B-CLL.
CONTEXT: This particular variant, called h in AceView
and in the article, was identified thanks to AceView.”
TaqmanTM real-time
quantitative PCR was used to quantitate expression of PANE1transcript
k (AceView) corresponding to
GenBank BQ056829, which encodes the epitope recognized by KSN-7A7,…
Blood. 2006 May 1;107(9):3779-86. Epub 2006 Jan 3.
121- Iterative gene prediction and pseudogene
removal improves genome annotation.
van
Baren MJ, Brent MR.
Genome Res. 2006 May; 16(5):
678-685.
Abstract | Full Text | PDF-489K |
120- Tumoral expression
of BRCA1, estrogen receptor alpha and ID4 protein in patients with sporadic
breast cancer.
CONTEXT: AceView is used as a source of information for
alternative splice variants.
Cancer Biol Ther. 2006 May;5(5):505-10. Epub 2006 May 13.
119- The Mlx Network:
Evidence for a Parallel Max-Like Transcriptional Network That Regulates Energy
Metabolism
Billin AN, Ayer DE
CONTEXT: AceView (www.ncbi.nlm.nih.gov/IEB/Research/Acembly) predicts nine alter- ... in the public databases for WBSCR14, and AceView predicts 13 different ...
Current
Topics in Microbiology and Immunology, Volume 302, pages 255-278, May 2006,
Springer Berlin Heidelberg
118- Spread of an
inactive form of caspase-12 in humans is due to recent positive selection.
Summary: The human caspase-12 gene is polymorphic for the presence or absence of a stop codon, which results in the occurrence of both active (ancestral) and inactive (derived) forms of the gene in the population. It has been shown elsewhere that carriers of the inactive gene are more resistant to severe sepsis…
CONTEXT: The seven
exons in the standard transcript (AceView) and an eighth exon (exon 3)
present in some splice variants (Fischer et al. 2002) were considered. ...
Am J Hum Genet. 2006 Apr;78(4):659-70. Epub 2006 Feb 21.
117- Dynamic spectrum quality assessment and iterative computational
analysis of shotgun proteomic data: toward more efficient identification of
post-translational modifications, sequence polymorphisms, and novel peptides.
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R.
SUMMARY: ..Spectra are not assigned to peptides for
diverse reasons. These include deficiencies of the scoring schemes … omissions
in the database searched, or the observation of sequences that are not
anticipated from the genomic sequence (e.g. splice forms, somatic
rearrangement, and processed proteins). To increase the amount of information
that can be extracted from proteomic MS/MS datasets, we developed a robust
method that detects high quality spectra…
CONTEXT: tryptic peptide LQGSATAAEAQVGHQTAR, is particularly
interesting, confirmed by Mascot (expectation value 5 10-5), present in several
predicted alternative splice forms of LIME1 from AceView gene models (November
2004. version), but not in the unique “standard” form of the NCBI Entrez
Protein sequence database (NP_060276).…. forms created based on the AceView
gene models. ... according to the AceView13 gene models (November 2004 ...
Mol Cell Proteomics. 2006 Apr;5(4):652-70. Epub 2005 Dec 12.
116- Transcriptional regulation of the human NRIP1/RIP140 gene by
estrogen is modulated by dioxin signalling.
Augereau P, Badia E, Fuentes M,
Rabenoelina F, Corniou M, Derocq D, Balaguer P, Cavailles V.
CONTEXT: In the abstract, the authors say: “We identified several noncoding exons with alternative splicing and localized the promoter region more than 100 kilobases upstream from the coding exon.” In reality, the complexity of the gene and distant promoters are directly from AceView, as acknowledged in figure 3, sequence of the promoter, (‘coordinates of the human sequence are given relative to the 5_-end of NRIP1 exon 1 as reported in the AceView database ..) but figure 2, the structure of the gene, is actually directly derived from AceView (2004 or 2005 versions).
Mol Pharmacol. 2006 Apr;69(4):1338-46. Epub 2006 Jan 3.
115- Reference based annotation with GeneMapper.
Chatterji S, Pachter L.
CONTEXT: Lack of genome wide, full length cDNA sequences for these species will make it virtually impossible to annotate these genomes completely using cDNA based methods such as Aceview [1]. Use of such information frequently requires alignment programs. In the case of cDNA, in order to make use of the evidence, programs such as Aceview [1], ecGene [15], GMAP [16], and BLAT [17] align cDNA with genomic sequence.
Genome Biol. 2006; 7(4): R29. published online before print April 5, 2006
Abstract | Full Text | PDF-434K | Supplementary Material |
114- Bovine NALP5,
NALP8, and NALP9 genes: assignment to a QTL region and the expression in adult
tissues, oocytes, and preimplantation embryos.
Ponsuksili
S, Brunner RM, Goldammer T, Kuhn C, Walz C, Chomdej S, Tesfaye D, Schellander
K, Wimmers K, Schwerin M.
CONTEXT: ..In agreement with the finding in human (AceView; http://. www.ncbi.nih.gov/IEB/ Research/Acembly), we found low. abundance of NALP8 and NALP5 transcripts in ...
Biol Reprod. 2006 Mar;74(3):577-84. Epub 2005 Dec 7.
113- A Third Approach to Gene Prediction Suggests Thousands of
Additional Human Transcribed Regions.
Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach JC, Hood L, Smit AF.
PLoS Comput Biol. 2006 Mar; 2(3): e18. published online before print March 17, 2006
Abstract | Full Text | PDF-0.7M | Supplementary Material |
112- Transcription factor YY1:
structure, function, and therapeutic implications in cancer biology.
Gordon S, Akopyan G, Garban H, Bonavida B.
CONTEXT: According to AceView database (http://www.ncbi.nih.gov/IEB/Re
search/Acembly/index.html), the sequence of the YY1 gene is supported by
850 sequences from 781 cDNA (accessed November 2004). The human YY1 gene
produces eight different transcripts (a, b, c, d, e, f, g, and h) generated by
alternative splicing, encoding eight different putative protein isoforms (three
complete, three COOH-complete, and two partial). The functional significance of
these isoforms remains elusive. There are two alternative promoters. Different
transcripts differ by truncation of the 5' end, truncation of the 3' end,
presence or absence of four cassette exons, and different boundaries on common
exons due to variable splicing of an internal intron.
Oncogene. 2006 Feb 23;25(8):1125-42. Review.
111- A novel and cytogenetically cryptic t(7;21)(p22;q22) in acute myeloid leukemia results in fusion of RUNX1 with the ubiquitin-specific protease gene USP42
K Paulsson, A
SUMMARY: Although many of the chromosomal abnormalities in hematologic malignancies are identifiable cytogenetically, some are only detectable using molecular methods. We describe a novel cryptic
CONTEXT: ...2 kb (Figure 2b). The first of these may correspond to the aAug05 transcript (http://www.ncbi.nih.gov/IEB/Research/Acembly/ ), which is 5093 bp and contains the sequences that hybridize to the USP42 blot probe. The latter transcript...
Leukemia 20, 224 - 229 (01 Feb 2006) Original Article
110- The Homologous Putative GTPases
Grn1p from Fission Yeast and the Human GNL3L Are Required for Growth and Play a
Role in Processing of Nucleolar Pre-rRNA.
CONTEXT: According to AceView (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly), these genes are expressed at 4.1 or very high (NGP-1), 3.2 or high (GNL3L), 0.8 or well expressed (NS) times the average gene (GNL-1 expression is moderate to low). We have examined three …
Du X, Rao MR, Chen XQ, Wu W,
Mahalingam S, Balasundaram D.
Mol Biol Cell. 2006 Jan; 17(1):
460-474.
Abstract | Full Text | PDF-0.7M | Supplementary Material |
109- In silico discovery of human natural antisense transcripts.
Li YY, Qin L, Guo ZM, Liu L, Xu H, Hao P, Su J, Shi Y, He
WZ, Li YX.
CONTEXT: Alternative splicing information was
obtained from AceView [33]. we checked the rest 400 hNAT pairs (568-168)
using AceView [33] and found that additional 367 NAT pairs involved splicing
variants (see Additional Table 2B)… (thanks
to AceView alternative variants, they show that)
SUMMARY: 77.4% (414/535) of the natural antisense genes have their pairing regions affected or completely eliminated by alternative splicing, suggesting significant relationship of alternative splicing and antisense-directed regulation.
BMC Bioinformatics. 2006; 7: 18. published online before print January 13, 2006
Abstract | Full Text | PDF-328K | Supplementary Material |
34 in 2005
108- Genome-wide assembly and analysis of alternative transcripts in mouse –
Consorcio
Madrono eText - Full-Text
Plus! –
AA Sharov, DB Dudekula, MSH Ko -
To build a mouse gene index with the most comprehensive coverage of alternative
transcription/splicing (ATS), we developed an algorithm and a fully automated
computational pipeline for transcript assembly from expressed sequences ...
Genome Research, 2005 -
107- Heterogeneous
expression of the aquaporin 1 (AQP1) water channel in tumors of the prostate,
breast, …
A Mobasheri, R Airley, SM Hewitt, D Marples -
... a Data from AceView
(http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly NCBI
August 2004). Chromosome locations from http://www.ncbi ...
Int J Oncol, 2005 - 147.52.72.117
106- Expression
of the GLUT1 and GLUT9 facilitative glucose transporters in embryonic
chondroblasts and … - BS
eText - Consorcio
Madrono eText - Full-Text
Plus! - all
3 versions »
A Mobasheri, H Dobson, SL Mason, F Cullingham, M … - CONTEXT:
... including placenta, lung, blood leukocytes, heart, and skeletal
muscle (Phay et al., 2000a) (updated information may be found on the NCBI AceView
site: http ...
Cell Biology International, 2005 - Elsevier
105- Genomic
duplication in Dyggve Melchior Clausen syndrome, a novel mutation mechanism in
an autosomal recessive disorder.
Kinning E, Tufarelli C, Winship WS, Aldred MA, Trembath RC.
CONTEXT: 6, 7 Dymeclin, the protein product of the DMC gene,
is widely expressed and several splicing isoforms have been predicted (Aceview,
NCBI), and. differentially sized transcripts seen on northern blot. 6. The.
longest open reading frame ...
J Med Genet. 2005 Dec;42(12):e70.
104- Deletion of the
ANKRD15 gene at 9p24.3 causes parent-of-origin-dependent inheritance of
familial cerebral palsy.
Lerer I, Sagi M, Meiner V, Cohen T,
Zlotogora J, Abeliovich D.
CONTEXT: “Other alternative transcripts may
exist according to the analysis of the identified cDNAs clones and
the genomic DNA (AceView, NCBI).”
Then, to conclude: “The mode of the ANKRD15 expression supports the view of a complex locus with more than one promoter and several different transcripts that may code for different proteins.”
Hum Mol Genet. 2005 Dec 15;14(24):3911-20. Epub 2005 Nov 21.
103- Molecular
cloning and expression of novel alternatively spliced cytochrome P450 2E1 mRNAs
in humans
Mario Bauer, Olf Herbarth, Gabi Aust and Carolin Graebsch
CONTEXT: NCBI
AceView lists 10 transcripts for CYP2E1 in detail. Surprisingly,
none of these transcripts was identical to the three new isoforms, because they
did not contain skipped exons. The sequences of the 10 CYP2E1
transcripts were supported by 155 sequences from 135 cDNA clones.
And the clones were obtained from different human
tissues like
hepatocellular carcinoma, dorsal root ganglia, chondrosarcoma, brain and fetal
liver. That means, great efforts of such cloning strategies are not sufficient
to detect
the new isoforms, which
were spread through the human tissues and discovered by the PCR technique.
Note: the authors are right: we are still far from saturation in cDNA clones!
Molecular
and Cellular Biochemistry, Volume 280, Numbers
1-2 / December, 2005, pages 201-207
102- CLAMP, a novel microtubule-associated protein with
EB-type calponin homology.
Dougherty
GW, Adler HJ, Rzadzinska A, Gimona M, Tomita Y, Lattig MC, Merritt RC Jr,
Kachar B.
CONTEXT: sapiens (C20orf28, DUF1042.0; NCBI Aceview), Dr, Danio Rerio. (AAH55652), and Gl, Giardia lamblia (EAA36800). Amino acid resi- ...
Cell Motil Cytoskeleton. 2005 Nov;62(3):141-56. Erratum in: Cell Motil Cytoskeleton. 2005 Dec;62(4):259.
101- Loss-of-function
mutation of the AF9/MLLT3 gene in a girl with neuromotor development delay,
cerebellar ataxia, and epilepsy.
CONTEXT: According to AceView
(http://www.ncbi.nih.gov/. IEB/Research/Acembly/index.html), this gene is
expressed at very high level mostly in brain, muscles, liver, kidney and pancreas
...
Hum Genet. 2005 Oct;118(1):76-81. Epub 2005 Oct 28.
100- Antimetastatic
gene expression profiles mediated by retinoic acid receptor beta 2 in
MDA-MB-435 breast cancer cells.
Wallden B, Emond
M, Swift ME, Disis ML, Swisshelm K.
CONTEXT: expression differential obtained from the microarray analyses, we interrogated Map Viewer [30] or AceView [31] to determine if the 60-mer overlapped mRNA isoforms (e.g., splice variants) known for the gene of interest. AceView indicate that there are overlapping mRNA isoforms with the 60 mer probe. ...
BMC Cancer. 2005; 5: 140. published online before print October 28, 2005
Abstract | Full Text | PDF-0.5M | Supplementary Material |
99- ASPIC: a novel method to predict the
exon-intron structure of a gene that is optimally compatible to a set of
transcript sequences.
Bonizzoni
P, Rizzi R, Pesole G.
CONTEXT: A total of 1009
introns were predicted by ASPIC as compared to 753 by ASAP, 495 by ASD and 1194
by AceView. ASPIC predicted 95.7%, 93.1% and 75.8% of ...
BMC Bioinformatics. 2005; 6: 244.
published online before print October 5, 2005
Abstract | Full Text | PDF-0.7M | Supplementary Material |
98- Detecting seeded motifs in DNA sequences.
Pizzi
C, Bortoluzzi S, Bisognin A, Coppe A, Danieli GA.
Nucleic Acids Res. 2005; 33(15):
e135. published online before print September 1, 2005
Abstract | Full Text | PDF-105K |
97- Cloning and
characterization of the human glutathione synthetase 5’-flanking
region.
Lee T, Yang H, Whang J, Lu S.
CONTEXT: Using AceView. (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/),we compared our experimentally determined transcriptional start site with ...(AceView and confirmed AceView structural predictions) the start site determined in our study
is identical to GSS variants a, d and h (as identified by AceView).
Biochem J. 2005 Sep 1; 390(Pt 2):
521-528. published online before print August
23, 2005
Abstract
| Full
Text | PDF-0.6M
|
96- A high-resolution
map of active promoters in the human genome.
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA,
CONTEXT: see supplementary material, AceView was instrumental in defining putative promoters, which were mainly confirmed!
Nature. 2005 Aug 11;436(7052):876-80. Epub 2005 Jun 29.
95- Loss of ZDHHC15 expression in a woman with a balanced translocation t(X;15)(q13.3;cen) and severe mental retardation
Mahmoud Reza Mansouri, Lena Marklund, Peter Gustavsson, Edward Davey, Birgit Carlsson, Catharina Larsson, Irene White, Karl-Henrik Gustavson, Niklas Dahl
CONTEXT: ...of the first exon of the gene ZDHHC15 (Figure 2c). The ZDHHC15 gene According to the NCBI Aceview database (www.ncbi.nlm.nih.gov/AceView ), the ZDHHC15 gene is predicted based on alignment of mRNA and ESTs to genomic sequences. The...
European Journal of Human Genetics 13, 970 - 977 (01 Aug 2005) Article
94- Differential Gene
Expression in the Auditory System
Irene S. Gabashvili, Richard J. Carter, Peter Markstein and Anne B.S. Giersch
CONTEXT: AceView database [15] and are. being incorporated into the next ... functional annotation of cDNA-supported genes in higher organisms using AceView, ...
Lecture Notes in Computer Science; Volume 3594/2005, page 1-8. Advances in Bioinformatics and Computational Biology (Springer Berlin / Heidelberg) August 29, 2005.
93- Variants of ENPP1 are associated with childhood and
adult obesity and increase the risk of glucose intolerance and type 2 diabetes
David Meyre, Nabila Bouatia-Naji, Agnès Tounian, Chantal Samson, Cécile Lecoeur, Vincent Vatin, Maya Ghoussaini, Christophe Wachter, Serge Hercberg, Guillaume Charpentier, Wolfgang Patsch, François Pattou, Marie-Aline Charles, Patrick Tounian, Karine Clément, Béatrice Jouret, Jacques Weill, Betty A Maddux, Ira D Goldfine, Andrew Walley, Philippe Boutin, Christian Dina, Philippe Froguel
SUMMARY: We identified a locus on chromosome 6q16.3–q24.2 (ref. 1) associated with childhood obesity that includes 2.4 Mb common to eight genome scans for type
CONTEXT: ...beta cells. Taking into account that five ENPP1
isoforms are known (
...URLs.
Nature Genetics 37, 863 - 867 (01 Aug 2005) Letters
92- GREB1
is a critical regulator of hormone dependent breast cancer growth
Rae JM, Johnson MD, Scheys JO, Cordero KE, Larios JM, Lippman ME.
CONTEXT: The longest GREB1 transcript codes for a putative 1949-aa protein with at least four transmembrane domains and a N-myristoylation domain (http://www.ncbi.nlm. nih.gov/IEB/Research/Acembly). Gosh et al. were the first to show that GREB1 is an estrogen regulated gene..
Breast Cancer Res Treat. 2005 Jul;92(2):141-9.
91- ASePCR:
alternative splicing electronic RT-PCR in multiple tissues and organs.
Kim N, Lim D, Lee S, Kim H.
Nucleic Acids Res. 2005 Jul 1; 33(Web Server
issue): W681-W685. published online before
print June 27, 2005
Abstract | Full Text | PDF-428K |
90- Genome-Wide Analysis of Chromosomal Features Repressing
Human Immunodeficiency Virus Transcription.
Lewinski MK, Bisgrove D, Shinn P,
Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD.
J Virol. 2005 Jun; 79(11):
6610-6619.
Abstract | Full Text | PDF-1M | Supplementary Material |
89- Barth syndrome:
TAZ gene mutations, mRNAs, and evolution.
CONTEXT: Database
mining [AceView. genes at www.ncbi.nih.gov] also revealed a multitude of
TAZ. cDNA sequences consisting of various combinations of exons ...
Am J Med Genet A. 2005 May 1;134(4):409-14.
88- A multistep bioinformatic approach detects putative
regulatory elements in gene promoters.
Bortoluzzi
S, Coppe A, Bisognin A, Pizzi C, Danieli GA.
CONTEXT: Sequences were then searched by BLAT [40] against release 15 of human genome sequence, for prediction of Transcription Start Site (TSS), obtained by analysis of mRNA/genomic DNA alignment, 5' ESTs placement and Acembly gene boundaries [41] annotation.
BMC Bioinformatics. 2005; 6: 121.
published online before print May 18, 2005
Abstract | Full Text | PDF-361K | Supplementary Material |
87- Redefinition of Affymetrix probe sets by
sequence overlap with cDNA microarray probes reduces cross-platform
inconsistencies in cancer-associated gene expression measurements.
Carter SL, Eklund AC, Mecham BH,
Kohane IS, Szallasi Z.
CONTEXT: For a given
Affymetrix platform, all probe sequences as obtained from Affymetrix were
matched against the Acembly transcript database. ...
BMC Bioinformatics. 2005; 6: 107.
published online before print April 25, 2005
Abstract | Full Text | PDF-437K | Supplementary Material |
86- ECgene: Genome-based EST clustering and
gene modeling for alternative splicing.
Kim N, Shin S, Lee S.
Genome Res. 2005 Apr; 15(4):
566-576.
| PubLink |
85- A novel splice
variant of human gene NPL, mainly expressed in human liver, kidney and
peripheral blood leukocyte.
Wu M, Gu S, Xu J, Zou X, Zheng H, Jin Z, Xie Y, Ji C, Mao Y
CONTEXT: Subsequent editing and assembly of all the sequences from one clone was performed using Acembly (ftp://ftp.sanger.ac.uk/pub/acedb).
DNA Seq. 2005 Apr;16(2):137-42.
84- Expression of the
Leo1-like domain of replicative senescence down-regulated Leo1-like (RDL)
protein promotes senescence of 2BS fibroblasts.
CONTEXT: why intact RDL has no apparent effect on senescence while Leo and RDL-Leo– has clear and opposite effects, and why such two counteractive domains (Leo1-like domain and AAA domain) would be integrated into one molecule during evolution. There are several hypotheses .. Aceview analysis of RDL-related sequences (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly), the gene might have six different transcripts produced by alternative splicing. The difference among these proposed transcripts includes truncation of the 3' end, presence or absence of five cassette exons, and common exons with different boundar…
FASEB J. 2005 Apr;19(6):521-32.
83- SNPHunter: a
bioinformatic software for single nucleotide polymorphism data acquisition and
management.
Wang L, Liu S,
Niu T, Xu X.
CONTEXT: Once the starting
and ending coordinates of a particular gene are determined by SNPHunter through
NCBI's AceView, the 5' upstream and 3' downstream regions ...
Gene statistics from NCBI AceView; number of exons was calculated as number of intron plus 1.
BMC Bioinformatics. 2005; 6: 60. published online before print March 18, 2005
Abstract | Full Text | PDF-482K |
82- Distribution of
AQP2 and AQP3 water channels in human tissue microarrays.
Mobasheri
A, Wray S, Marples D.
CONTEXT: According to the information available on the NCBI AceView website1
(complied July 2003) the aquaporin family consists of at least twelve small
integral membrane proteins (AQP0-AQP11) with high homology to the major
intrinsic protein also known as MIP or AQP0 (Verkman 2003)
J Mol Histol. 2005
Feb;36(1-2):1-14.
PMID: 15703994
81- The domain
architecture of large guanine nucleotide exchange factors for the small
GTP-binding protein Arf.
Mouratou B, Biou V, Joubert A, Cohen J, Shields DJ, Geldner N, Jürgens G, Melançon P, Cherfils J.
CONTEXT: Splice variants for hGBF1, hBIG1 and hBIG2 were identified from information provided under Aceview in the December (03) release …
BMC Genomics. 2005; 6: 20. published online before print February 17, 2005
| Abstract | Full Text | PDF-0.8M |
80- Gene expression signature for angiogenic and nonangiogenic non-small-cell lung cancer
Jiangting Hu, Fabrizio Bianchi, Mary Ferguson, Alfredo Cesario, Stefano Margaritora, Pierluigi Granone, Peter Goldstraw, Michelle Tetlow, Cathy Ratcliffe, Andrew G Nicholson, Adrian Harris, Kevin Gatter, Francesco Pezzella
CONTEXT: ...average linkage method. Unless otherwise stated, the LocusLink database and its links to Unigene, OMIM, GenBank and Aceview databases, available at the NCBI home page (www.ncbi.nlm.nih.gov ), were used to identify all known human...
Oncogene 24, 1212 - 1219 (10 Feb 2005) Original Paper
79- EST-BASED ANALYSIS OF GENE EXPRESSION IN THE HUMAN COCHLEA
File Format: PDF/Adobe
Acrobat
“Identification and functional. annotation of cDNA-supported genes in higher.
organisms. using. AceView,. unpublished. http://www.aceview.org/ ...
ieeexplore.ieee.org/iel5/10336/32899/01540547.pdf?arnumber=1540547
78- Identification of a new locus for isolated familial keratoconus at 2p24.
Hutchings H, Ginisty H, Le Gallo M, Levy D, Stoesser F, Rouland JF, Arne JL, Lalaux MH, Calvas P, Roth MP, Hovnanian A, Malecaze F
CONTEXT: This candidate region contains eight known genes
and 10 Acembly gene predictions. ... The Acembly gene
predictions correspond to spliced Image clones and ...
J Med Genet. 2005 Jan;42(1):88-94.
77- Characterization
of the human MDR1 gene.
Bodor M, Kelly
EJ, Ho RJ.
CONTEXT: …org) enumerates 29 exons within the gene, while Aceview. (www.ncbi.nih.gov/IEB/Research/Acembly) computational. analysis predicts 29 exons with 18 ...
AAPS J. 2005 Feb 16;7(1):E1-5.
30 in 2004
76- GeneTide-Terra Incognita Discovery Endeavor: a new transcriptome
focused member of the GeneCards/GeneNote suite of databases.
Shklar M, Strichman-Almashanu L, Shmueli O, Shmoish M, Safran M, Lancet D.
CONTEXT: ... genomic resources including UniGene, DoTS, AceView and in-house resources. GeneTide thus creates comprehensive links between ESTs and GeneCards genes. ...
Nucleic Acids Res. 2005 Jan 1; 33(Database
Issue): D556-D561. published online before
print December 17, 2004
Abstract
| Full
Text | PDF-0.8M
| Supplementary
Material |
75- ECgene: genome annotation for alternative
splicing.
Kim P, Kim N, Lee Y, Kim B, Shin
Y, Lee S.
CONTEXT: …AceView at
the NCBI is another website that provides ample information on
alternatively spliced genes (D. Thierry-Mieg, J. Thierry-Mieg, M. Potdevin and
M. ...
Nucleic Acids Res. 2005 Jan 1;
33(Database Issue): D75-D79. published online before print December 17, 2004
74- Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line.
Wahl MB, Caldwell RB, Kierzek AM, Arakawa H, Eyras E, Hubner N, Jung C, Soeldenwagner M, Cervelli M, Wang YD, Liebscher V, Buerstedde JM.
CONTEXT: ... sequences in the human transcriptome are reported to be over 2000 bps according to NCBI's AceView database http://www.ncbi.nih.gov/IEB/Research/Acembly/ ...
BMC Genomics. 2004; 5: 98. published online before print December 21, 2004
73- Fine mapping and identification of a candidate gene SSH1 in disseminated superficial actinic porokeratosis.
CONTEXT: According to acembly/aceview, there are 9 different
alternative transcripts of SSH1 (i.e., aDec03, bDec03, cDec03, dDec03,
eDec03, fDec03, hDec03, jDec03). We found a frame shift mutation, c.
fDec03:56_57del (p.Ser19CysfsX24), in splice variant f of SSH1 in all
affected individuals of family 3, and another frame shift mutation,
c.fDec03:85_88del (p.Pro27ProfsX54), in the same alternative variant in one
non-familial DSAP case. .. the mutated exon is not in the RefSeq but is in a specific alternative exon in AceView.
Hum Mutat. 2004 Nov;24(5):438.
72- Identification of
an evolutionarily conserved domain in human lens epithelium-derived growth
factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase.
Cherepanov P, Devroe E, Silver PA,
Engelman A.
CONTEXT: Discussion: Sequences derived from 215 cDNA clones suggesting several alternative LEDGF splice variants exist in the AceView data base (for up to date information consult www.ncbi.nlm.nih.gov/IEB/Research/Acembly/). While the most abundant splice form, supported by 170 cDNA clones, encodes for LEDGF/p75, only 12 ..
J Biol Chem. 2004 Nov 19;279(47):48883-92. Epub 2004 Sep 14.
71- Human cannabinoid receptor 1: 5' exons, candidate regulatory regions, polymorphisms, haplotypes and association with polysubstance abuse
P-W Zhang, H Ishiguro, T Ohtsuki, J Hess, F Carillo, D Walther, E
CONTEXT: ...unclear. Current Genbank CB1/Cnr1 cDNA variants are termed 1 (5.4 kb; gi15208646) and 2 (1.2 kb; gi15208647). Aceview lists a similar CB1/Cnr1 mRNA 'a' variant as well as 'b' variant of 1868 bp. Both databases indicate shifted open... 38 On this background , current Aceview CB1 / Cnr1 depictions with short 5 ' UTR ...
Molecular Psychiatry 9, 916 - 931 (01 Oct 2004) Original Article
70- Identification of Mammalian microRNA Host Genes and
Transcription Units.
Rodriguez A, Griffiths-Jones S,
Ashurst JL, Bradley A.
Genome Res. 2004 Oct; 14(10a):
1902-1910.
PubLink |
69- C. elegans ORFeome Version 3.1: Increasing the Coverage
of ORFeome Resources With Improved Gene Predictions.
Lamesch P, Milstein S, Hao T,
Rosenberg J, Li N, Sequerra R, Bosak S, Doucette-Stamm L, Vandenhaute J, Hill
DE, Vidal M.
Genome Res. 2004 Oct; 14(10b):
2064-2069.
PubLink |
68- Mutation of GATA3 in human breast tumors
Jerry Usary, Victor Llaca, Gamze Karaca, Shafaq Presswala, Mehmet
Karaca, Xiaping He, Anita Langerød, Rolf K
resen,
Daniel S Oh, Lynn G Dressler, Per E Lønning, Robert L Strausberg, Stephen
Chanock, Anne-Lise Børresen-Dale, Charles M Perou
CONTEXT: ...to encode a 48 kDa protein that is known to undergo alternative splicing (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html ). By Western blot analysis, we identified the expected 48 kDa band as well as a smaller...
Oncogene 23, 7669 - 7678 (07 Oct 2004) Original Paper
67- A comprehensive transcript index of the human genome
generated using microarrays and computational approaches.
Schadt EE, Edwards SW,
GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A,
Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M,
Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker
DD.
CONTEXT: The NCBI Acembly
alternative splicing predictions further suggest the presence of additional
isoforms of this gene (see Figure 4). ...
confirmed by the microarray experiments..
Genome Biol. 2004; 5(10): R73.
published online before print September 23, 2004
Abstract | Full Text | PDF-0.7M | Supplementary Material |
66- DEAD-box RNA
helicases in Arabidopsis thaliana: establishing a link between quantitative expression,
gene structure and evolution of a family of genes.
Mingam
A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M, Lecharny A.
CONTEXT: ... by the Ace.mbly sequence assembly package (T. Mieg et al., http:/ / www.aceview.org ) of 210 388 partial or full-length transcripts with chromosomes. Promoter analysis. Upstream sequences of genes were retrieved from ...
Plant Biotechnol J. 2004 Sep;2(5):401-15.
65- Retroviral DNA Integration: ASLV, HIV, and MLV Show
Distinct Target Site Preferences.
Mitchell RS, Beitzel BF, Schroder
AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD.
PLoS Biol. 2004 Aug; 2(8): e234.
published online before print August 17, 2004
Abstract | Full Text | PDF-0.6M | Supplementary Material |
64- The Ras-related protein AGS1/RASD1 suppresses cell
growth
Govindan Vaidyanathan, Mary J Cismowski, Guoshun Wang, Timothy S Vincent, Kevin D Brown, Stephen M Lanier
CONTEXT: ...(Figure 1a, b) (Tu and Wu, 1999; Kemppainen et al., 2003, http://www.ncbi.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=33&term=ags1 ). (Vaidyanathan G, Hill SM and SM Lanier. The expression of AGS1/RASD1 in MCF-7...
Oncogene 23, 5858 - 5863 (29 Jul 2004) Short Report
63- Clathrin Isoform CHC22, a Component of Neuromuscular and Myotendinous Junctions, Binds Sorting Nexin 5 and Has Increased Expression during Myogenesis and Muscle Regeneration.
Towler MC, Gleeson PA, Hoshino S, Rahkila P, Manalo V, Ohkoshi N, Ordahl C, Parton RG, Brodsky FM.
Mol Biol Cell. 2004 Jul; 15(7): 3181-3195.
Abstract | Full Text | PDF-1.6M | Supplementary Material |
62- ASmodeler: gene modeling of
alternative splicing from genomic alignment of mRNA, EST and protein sequences.
Kim N, Shin S, Lee S.
CONTEXT: n addition to the
user-supplied sequences, UniGene clusters and many well-known gene predictions
such as Genscan, Ensembl and Acembly may be included in ...
Nucleic Acids Res. 2004 Jul 1;
32(Web Server issue): W181-W186.
Abstract | Full Text | PDF-448K |
61- CGI-58 interacts
with perilipin and is localized to lipid droplets. Possible involvement of
CGI-58 mislocalization in Chanarin-Dorfman syndrome.
Yamaguchi
T, Omatsu N, Matsushita S, Osumi T.
CONTEXT: database analysis in AceView of NCBI, several variants of human CGI-58 are. predicted. These results indicate that protein expression of CGI-58 is induced ...
J Biol Chem. 2004 Jul 16;279(29):30490-7. Epub 2004 May 10.
60- Refined genetic mapping of autosomal recessive chronic distal spinal muscular atrophy to chromosome 11q13.3 and evidence of linkage disequilibrium in European families
Louis Viollet, Mohammed Zarhrate, Isabelle Maystadt, Brigitte Estournet-Mathiaut, Annie Barois, Isabelle Desguerre, Michèle Mayer, Brigitte Chabrol, Bruno LeHeup, Veronica Cusin, Thierry Billette de Villemeur, Dominique Bonneau, Pascale Saugier-Veber, Anne Touzery-de Villepin, Anne Delaubier, Jocelyne Kaplan, Marc Jeanpierre, Joshué Feingold, Arnold Munnich
CONTEXT: ...protein domains are available at the Pfam protein family database and protein function from the Acembly/Aceview database). Amino-acid sequence alignments to the human and rodent databases failed to detect any homology to the known...
European Journal of Human Genetics 12, 483 - 488 (01 Jun 2004) Article
59- Immunohistochemical
localization of aquaporin 10 in the apical membranes of the human ileum: a
potential pathway for luminal water and small solute absorption.
Mobasheri A, Shakibaei M, Marples D.
CONTEXT: AceView website. 1. (complied July 2003)
AQP10 belongs. to the AQP family which consists of at least ...
33&c=Gene&l=AQP10, NCBI AceView, April 2003 ... AceView
was intensely used as background gene description in this article.
Table I. Expression, function, chromosome location, phenotype and tissue localization of the AQP1 protein.a aData from AceView (http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly NCBI August 2004).
Histochem Cell Biol. 2004 Jun;121(6):463-71. Epub 2004 Jun
8.
58- Lithium-calcium exchange is mediated by a distinct potassium-independent sodium-calcium exchanger.
CONTEXT: Based on the NCBI sequence annotation (www.ncbi.nlm.nih.gov/IEB/Research/Acembly), one set of primers was
designed to enhance the longest deduced open reading…
J Biol Chem. 2004 Jun 11;279(24):25234-40. Epub 2004 Apr 1.
57- An activated 5' cryptic splice site in the human ALG3 gene
generates a premature termination codon insensitive to nonsense-mediated mRNA
decay in a new case of congenital disorder of glycosylation type Id (CDG-Id).
Denecke J, Kranz C, Kemming D, Koch HG,
Marquardt T.
CONTEXT: However, a regulatory function of the truncated protein or transcript might be considered. In fact, transcripts of the proteasome 26S subunit gene are known to be antisense to the 50 part of the ALG3 transcript, making mutual regulation at the transcript level conceivable (NCBI, Aceview Database, www.ncbi.nih.gov/IEB/Research/Assembly).
Hum Mutat. 2004 May;23(5):477-86.
56- Gene expression
profiling: from microarrays to medicine.
Weeraratna AT, Nagel JE, de Mello-Coelho
V, Taub DD.
CONTEXT: the retrieval of information about individual genes from the various online genomic databases such as LocusLink, OMIM, Aceview (www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ ), UniGene (www.ncbi.nlm.nih.gov/unigene), KEGG (www.genome.ad.jp/kegg/kegg2.html), and GeneCardsTM…
J Clin Immunol. 2004 May;24(3):213-24. Review.
55- Identification of
a novel candidate gene, CASC2, in a region of common allelic loss at chromosome
10q26 in human endometrial cancer.
CONTEXT: … mosura a to f, Acembly gene predictions with
Alt-Splicing…this
team confirmed the AceView alternative variants
Acembly gene predictions with Alt-Splicing; BC036393
and AK055184, GenBank human mRNAs. c: Structure. characterization of the gene
designed ...
Hum Mutat. 2004 Apr;23(4):318-26.
54- Molecular cloning and characterization of SGT1.2, a novel splice variant of Homo sapiens SGT1.
Zou X, Ji C, Wang L, Wu M, Zheng H, Xu J, Jin F, Gu S, Ying K, Xie Y, Mao Y.
CONTEXT: acembly/ACE-mbly.html). A new full-length
cDNA. of splice variant of Homo sapiens SGT1 that has been. termed SGT1.2 was
isolated during our large-scale ...confirming
AceView
DNA Seq. 2004 Apr;15(2):140-3. PDF
53- Identification in
2 independent samples of a novel schizophrenia risk haplotype of the
dystrobrevin binding protein gene (DTNBP1).
CONTEXT: DTNBP1is predicted
(by AceView) to have 13 exons and has at least
12
different known messenger RNA transcripts (Figure 1). We initially screened
6669 bases of genomic sequence of which3161were exonic. We extended our
mutation screen to the 4 putative promoter regions of DTNBP1, because
promoters are among (though are not the only) the most important regulatory
elements in a gene. A total of 7920 bases of putative promoter sequence were
screened, resulting in a further 9 SNPs.
SUMMARY:
a number of the meaningful SNPs were found in regions described only in AceView
annotation and might have been missed otherwise.
Arch Gen Psychiatry. 2004 Apr;61(4):336-44.
52- Bioinformatic
approaches for identification and characterization of olfactomedin related
genes with a potential role in pathogenesis of ocular disorders.
Mukhopadhyay
A, Talukdar S, Bhattacharjee A, Ray K.
Mol Vis. 2004 Apr 20;10:304-14.
51- Candidate regions of tumor suppressor locus on chromosome 9q31.1 in
gastric cancer.
Kakinuma
N, Kohu K, Sato M, Yamada T, Nakajima M, Akiyama T, Ohwada S, Shibanaka Y.
CONTEXT: genes by the gene prediction programs, such as Acembly, En-. sembl, Fgenesh ... clusters and predicted 4 candidate genes by the Acembly…
Int J Cancer. 2004 Mar;109(1):71-5.
50- Genetic alteration and gene expression modulation
during cancer progression.
Garnis C, Buys TP, Lam WL.
Mol Cancer. 2004; 3: 9. published
online before print March 22, 2004
Abstract | Full Text | PDF-2.2M |
49- TP53 polymorphism
is associated with increased risk of colorectal cancer and with reduced levels
of TP53 mRNA.
Gemignani F, Moreno V, Landi S, Moullan N,
Chabrier A, Gutierrez-Enriquez S, Hall J, Guino E, Peinado MA, Capella G,
Canzian F.
CONTEXT: …publicly available databases (http://www.ncbi.nih.gov/IEB/Re
search/Acembly/) do not detail splicing variants affecting exon 3.
Moreover, analysis of the sequence by using a couple of algorithms that predict
splice…the authors confirmed the absence
of alternative splicing in this region of TP53, thereby confirming AceView.
Oncogene. 2004 Mar 11;23(10):1954-6.
48- Expression of mRNAs for DNA
methyltransferases and methyl-CpG-binding proteins in the human female germ
line, preimplantation embryos, and embryonic stem cells.
Huntriss
J, Hinkins M, Oliver B, Harris SE, Beazley JC, Rutherford AJ, Gosden RG,
Lanzendorf SE, Picton HM.
CONTEXT:
Expression of the human DNMT3L gene in both
the human female germline and during preimplantation development was assessed
using primers that were designed to amplify DNMT3L transcript variants a, b,
and c (as described by the AceView facility, NCBI). These variants are
supported by cDNA clones…
Mol Reprod Dev. 2004 Mar;67(3):323-36.
47- Identification of the gene for vitamin K epoxide reductase
Tao Li, Chun-Yun
Chang, Da-Yun Jin, Pen-Jen Lin, Anastasia Khvorova, Darrel W. Stafford
SUMMARY: Vitamin K epoxide reductase (VKOR) is the target of warfarin, the most widely prescribed anticoagulant for thromboembolic disorders. Although estimated to prevent twenty strokes
CONTEXT: ...in the NCBI database supporting the gene gi:13124769 and representing seven different splicing patterns (NCBI AceView program). These are composed of all or part of two to four exons. They have no other obvious features that would...
Nature 427, 541 - 544 (05 Feb 2004) Letters to Editor
24 in 2003
46- A new gene-finding tool: using the Caenorhabditis elegans operons for identifying functional partner proteins in human cells.
CONTEXT: we confirmed the SL1 sequence, as also reported by
www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb_AceView&db_worm&term_mrp-1&submit_Go.
a, the SL2 sequence shown in b is trans-spliced before the 5’UTR
of the mrp-2 gene.
J Biol Chem. 2004 Feb 20;279(8):7136-46. Epub 2003 Nov 13.
45- ANTHRAX TOXIN
R. John Collier, John A.T. Young
CONTEXT: ... Acembly program, which aligns current mRNA and EST data to genomic
sequence to generate models for gene transcripts, predicts that there are
two additional CMG2 protein isoforms encoded by four other alternatively spliced
mRNA transcripts (see NCBI’s Aceview locus, 118429)…
Annual Review of Cell and Developmental Biology. Volume 19, Page 45-70, Nov 2003
Abstract
| Full
Text | PDF (416 KB) | PDF
44- A new X-linked
syndrome with agenesis of the corpus callosum, mental retardation, coloboma,
micrognathia, and a mutation in the Alpha 4 gene at Xq13.
Graham JM Jr, Wheeler P, Tackels-Horne D, Lin AE, Hall BD, May M, Short KM, Schwartz CE, Cox TC.
CONTEXT: The structure of the Alpha 4 gene (www.ncbi.nih.nlm/AceView; January 2003) indicates that these
two changes are located in the 5UTR
of this gene (Fig. 5c).
Am J Med Genet A. 2003 Nov 15;123(1):37-44.
43-
Question 7: How would an investigator easily find compiled information
describing the structure of a gene of interest? Is it possible to obtain the
sequence of any putative promoter regions?
CONTEXT: ...against the genome using BLAT. The Acembly Gene Predictions With Alt-splicing track is derived from the alignment of human mRNA and EST sequence data against the genome, using the program Acembly. This program attempts to find the...
Nature Genetics 35, 44 - 48 (01 Sep 2003) User's Guide
42- Question 1: How
does one find a gene of interest and determine that gene's structure? Once the
gene has been located on the map, how does one easily examine other genes in
that same region?
CONTEXT: ...The direction of transcription is indicated by the arrowheads on the introns. The tracks labeled Ensembl Genes, Acembly Genes, Twinscan, SGP Genes, and Genscan Genes are the results of gene predictions (see Question 7). Alignments of...
Nature Genetics 35, 9 - 17 (01 Sep 2003) User's Guide
41- Question 3: During a positional cloning project aimed at finding a human disease gene, linkage data have been obtained suggesting that the gene of interest lies between two sequence-tagged site markers. How can all the known and predicted candidate genes in this interval be identified? What BAC clones cover that particular region?
CONTEXT: ...Inheritance in Man (OMIM), PubMed, GeneCards and Mouse Genome Informatics (MGI; Fig. 3.3). Many tracks, including Acembly Genes, Ensembl Genes and Genscan Genes, indicate predicted genes (see Question 7).To view the full set of...
Nature Genetics 35, 21 - 28 (01 Sep 2003) User's Guide
Full Text | PDF | Rights and permissions |
40- NONSYNDROMIC SEIZURE DISORDERS: Epilepsy and the Use of the Internet to
Advance Research
Mark F. Leppert
and Nanda A. Singh
Annual Review of Genomics and Human Genetics. Volume 4, Page 437-457, Sep 2003
Abstract
| Full
Text | PDF (861 KB) | PDF
39- Reciprocal fusion transcripts of two novel Zn-finger
genes in a female with absence of the corpus callosum, ocular colobomas and a
balanced translocation between chromosomes 2p24 and 9q32
Melissa B Ramocki, James Dowling, Inessa Grinberg, Virginia E Kimonis, Carlos Cardoso, Alyssa Gross, June Chung, Christa Lese Martin, David H Ledbetter, William B Dobyns, Kathleen J Millen
CONTEXT: ... represented by 11 exons across approximately 83 kb of genomic DNA encoding 6 C2H2-type Zn-fingers, two nuclear localization domains and a putative ER-membrane domain (AceView KIAA1803)…
European Journal of Human Genetics 11, 527 - 534 (01 Jul 2003) Original Article
38- Spotted Long Oligonucleotide Arrays for
Human Gene Expression Analysis.
Barczak A, Rodriguez MW, Hanspers
K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ.
Genome Res. 2003 Jul; 13(7):
1775-1785.
PubLink |
37- Identification of Promoter Regions in the Human Genome
by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay.
Khambata-Ford S, Liu Y, Gleason C,
Dickson M, Altman RB, Batzoglou S, Myers RM.
Genome Res. 2003 Jul; 13(7):
1765-1774.
PubLink
|
36- Alternatively
spliced isoforms of the human constitutive androstane receptor.
Auerbach SS,
Ramsden R, Stoner MA, Verlinde C, Hassett C, Omiecinski CJ.
Nucleic Acids Res. 2003 Jun 15; 31(12):
3194-3207.
| Abstract
| Full
Text | PDF-0.6M
|
35- C. elegans ORFeome
version 1.1: experimental verification of the genome annotation and resource
for proteome-scale protein expression
Jérome Reboul, Philippe Vaglio, Jean-François Rual, Philippe Lamesch, Monica Martinez, Christopher M. Armstrong, Siming Li, Laurent Jacotot, Nicolas Bertin, Rekin's Janky, Troy Moore, James R. Hudson, James L. Hartley, Michael A. Brasch, Jean Vandenhaute, Simon Boulton, Gregory A. Endress, Sarah Jenna, Eric Chevet, Vasilis Papasotiropoulos, Peter P. Tolias, Jason Ptacek, Mike Snyder, Raymond Huang, Mark R. Chance, Hongmei Lee, Lynn Doucette-Stamm, David E. Hill, Marc Vidal
CONTEXT: ...these two cycles were not included in the ORFeome analysis. We aligned OSTs on the C. elegans genome sequence using Acembly. The combined sequence information from 5' and 3' OSTs covered the ORF sequence fully or partially for 6,335...
Nature Genetics 34, 35 - 41 (01 May 2003) Article
34- Triple analysis of the cancer
epigenome: an integrated microarray system for assessing gene expression, DNA
methylation, and histone acetylation.
Shi H, Wei SH, Leu YW, Rahmatpanah F, Liu JC, Yan PS, Nephew KP, Huang TH.
Cancer Res. 2003 May 1;63(9):2164-71.
33- Assembling a View of the Human Genome
Colin A. M. Semple
CONTEXT: Acembly predictions find all the FOXP2
exons that we know are present from U80741, at ... This is carried out by a program called Acembly (unpublished data; ...
Chapter in Bioinformatics
for Geneticists, Published Online: 22 May 2003; Editor(s):
Michael R. Barnes, Ian C. Gray
32- Identification of
mutations in a new gene encoding a FERM family protein with a pleckstrin
homology domain in Kindler syndrome.
Jobard
F, Bouadjar B, Caux F, Hadj-Rabia S, Has C, Matsuda F, Weissenbach J, Lathrop
M, Prud'homme JF, Fischer J.
Hum Mol Genet. 2003 Apr 15;12(8):925-35.
31- Human capillary morphogenesis protein 2 functions as an
anthrax toxin receptor.
Scobie HM, Rainey GJ, Bradley KA,
Young JA.
CONTEXT: NCBI's ACEMBLY
program, which aligns current mRNA and EST data to genomic DNA sequence to
predict all possible gene transcript models, indicates that there .....
with amino acid residues 1-290, matching those of CMG2488 and CMG2489 but
lacking a transmembrane domain (see NCBI's AceView, locus 118429, sv 4
(g). ...
Proc Natl Acad Sci U S A. 2003 Apr
29; 100(9): 5170-5174. published online before print April 16, 2003
Abstract | Full Text | PDF-257K |
30- Protein prenyltransferases.
Maurer-Stroh S, Washietl S,
Eisenhaber F.
CONTEXT: AceView
[http://www.humangenes.org]. Alignment of expressed sequence tags and mRNAs to
the human genome, showing alternative splice forms. ... Automatic
comparisons of data from expressed sequence tags (ESTs) with genes (for example
using the program Acembly, for which the results are available ...
Genome Biol. 2003; 4(4): 212.
published online before print April 1, 2003
Abstract | Full Text | PDF-0.8M |
29- GALA, a Database for Genomic Sequence Alignments and
Annotations.
Giardine B, Elnitski L, Riemer C,
Makalowska I, Schwartz S, Miller W, Hardison RC.
Genome Res. 2003 Apr 1; 13(4):
732-741.
| PubLink |
28- LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale
Multiple Alignment of Genomic DNA.
Brudno M, Do CB, Cooper GM, Kim
MF, Davydov E, Program NC, Green ED, Sidow A, Batzoglou S.
Genome Res. 2003 Apr 1; 13(4):
721-731.
PubLink |
27- Characterization of the MLL partner gene AF15q14
involved in t(11;15)(q23;q14)
Martin U Kuefer, Vandana Chinwalla, Nancy J Zeleznik-Le, Frederick G Behm, Clayton W Naeve, Karen M Rakestraw, Suraj T Mukatira, Susana C Raimondi, Stephan W Morris
SUMMARY: Translocations interrupting the mixed lineage leukemia gene (MLL) occur in 7–10% of acute lymphoblastic leukemia (ALL) and 5–6% of acute myeloid leukemia (AML) cases.
CONTEXT: ...sequences yet to be identified. Indeed, UCSC Genome Browser (http://www.genome.ucsc.edu ) and AceView (http://www.ncbi.nih.gov/AceView ) predictions of the AF15q14 genomic structure suggest the existence of possible additional exons...
Oncogene 22, 1418 - 1424 (06 Mar 2003) Short Report
26- The UCSC Genome Browser Database.
Karolchik D, Baertsch R, Diekhans
M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ,
Weber RJ, Haussler D, Kent WJ.
Nucleic Acids Res. 2003 Jan 1;
31(1): 51-54.
| Abstract | Full Text | PDF-0.8M |
25- WorfDB: the Caenorhabditis elegans ORFeome Database.
Vaglio P, Lamesch P, Reboul J,
Rual JF, Martinez M, Hill D, Vidal M.
Nucleic Acids Res. 2003 Jan 1;
31(1): 237-240.
Abstract | Full Text | PDF-0.8M |
24- Ensembl 2002: accommodating comparative genomics.
Clamp M, Andrews D, Barker D,
Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R,
Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H,
Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S,
Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A,
Vastrik I, Birney E.
Nucleic Acids Res. 2003 Jan 1;
31(1): 38-42.
Abstract | Full Text | PDF-0.9M |
23- Cloning and
characterization of a novel splicing variant of the ZADH1 gene.
CONTEXT: Each part of the
subsequent editing and assembly of all of the sequences from one clone was
performed using Acembly (
Cytogenet Genome Res. 2003;103(1-2):79-83.
7 in 2002
22- A novel mutation
disrupting the cytoplasmic domain of CRB1 in a large consanguineous family of
Palestinian origin affected with Leber congenital amaurosis.
CONTEXT: .. Interestingly, the ‘Acembly Gene Predictions with alt Splicing’
program, available from the Human Genome Working Draft at UCSC,
revealed that several expressed sequence tags contained the originally
reported exons 9, 10, and 11 and an additional CRB1 exon at the 3¢ end
(sequences Chr1_592_3603b, c, and d, respectively).This prediction was
confirmed by sequencing of the 1238-bp fragment amplified from
reverse-transcribed retinal mRNA using a forward primer designed….
Ophthalmic Genet. 2002 Dec;23(4):225-35.
21- The mouse mahoganoid coat color mutation disrupts a
novel C3HC4 RING domain protein.
Phan LK, Lin F, LeDuc CA, Chung
WK, Leibel RL.
J Clin Invest. 2002 Nov 15;
110(10): 1449-1459.
| Abstract | Full Text | PDF-2.6M |
20- Mutation of TBCE causes hypoparathyroidism–retardation–dysmorphism and autosomal recessive Kenny–Caffey syndrome
Ruti Parvari, Eli Hershkovitz, Nili Grossman, Rafael Gorodischer, Bart Loeys, Alexandra Zecic, Geert Mortier, Simon Gregory, Reuven Sharony, Marios Kambouris, Nadia Sakati, Brian F. Meyer, Aida I. Al Aqeel, Abdul Karim Al Humaidan, Fatma Al Zanhrani, Abdulrahman Al Swaid, Johara Al Othman, George A. Diaz, Rory Weiner, K. Tahseen S. Khan, Ronald Gordon, Bruce D. Gelb
CONTEXT: ...that corresponded largely to the
Nature Genetics 32, 448 - 452 (01 Nov 2002) Letters
19- A Gene Mutated in
Nephronophthisis and Retinitis Pigmentosa Encodes a Novel Protein,
Nephroretinin, Conserved in Evolution
Edgar Otto, Julia Hoefele, Rainer Ruf, Adelheid M. Mueller, Karl S. Hiller, Matthias T. F. Wolf, Maria J. Schuermann, Achim Becker, Ralf Birkenhäger, Ralf Sudbrak, Hans C. Hennies, Peter Nürnberg, and Friedhelm Hildebrandt
CONTEXT: Boxes
above the sequence delimit motifs as predicted by the programs given in parenthesis:
NLS = nuclear localization domain (ACEVIEW); ER = endoplasmic ...
The American Journal of Human Genetics, volume 71 (2002), pages 1161–1167
18- DATABASES AND TOOLS FOR
BROWSING GENOMES
Ewan Birney, Michele Clamp,, Tim Hubbard
CONTEXT: The Acembly program predicts gene structures from cDNAs and ESTs and is built ... In these cases Acembly will only keep multiple alignments if they are of ...
Annual Review of Genomics and Human Genetics. Volume 3, Page 293-310, Sep 2002
Abstract
| Full
Text | PDF (488 KB) |
17- Cloning, expression and characterization of a novel human VMP gene.
Cheng C, Xu J, Ye X, Dai J, Wu Q, Zeng L, Wang L, Zhao W, Ji C, Gu S, Xie Y, Mao Y.
CONTEXT: the insert was sequenced at least three times
bidirectionally. Subsequent editing and assembly of all the sequences from one
clone was performed using Acembly (Sanger’s Center).
Mol Biol Rep. 2002 Sep;29(3):281-6.
16- The Human Genome Browser at UCSC.
Kent WJ, Sugnet CW, Furey TS,
Roskin KM, Pringle TH, Zahler AM, Haussler AD.
Genome Res. 2002 Jun; 12(6):
996-1006.
PubLink |
12 in 2001
15- Meeting
Highlights:
Jo Wixon 1 *, Jennifer Ashurst 2, Jo Dicks
CONTEXT: …AceView, a tool that defines gene structure using cDNA and EST data. AceView aligns partial or complete mRNA sequences onto the genome…
Comparative and Functional Genomics, Volume 2, Issue 6, Pages 376-383; 26 Oct 2001
14- A protein–protein interaction map of the Caenorhabditis
elegans 26S proteasome
Anne Davy, Paul Bello, Nicolas Thierry-Mieg, Philippe Vaglio, Joseph Hitti, Lynn Doucette-Stamm, Danielle Thierry-Mieg, Jérome Reboul, Simon Boulton, Albertha J.M. Walhout, Olivier Coux, Marc Vidal
CONTEXT: ...was built based on a selected subset of the WormBase data and used in conjunction with the Acembly software (http://alpha.crbm.cnrs-mop.fr/acembly/) to align all insert sequences with the C. elegans genome for identification and to...
EMBO Reports 2, 821 - 828 (01 Sep 2001)
13- GENOME ANNOTATION:
FROM SEQUENCE TO BIOLOGY
CONTEXT: ...has been accelerated significantly by automated procedures for reconciling EST alignments with gene predictions (ACEmbly, J. Thierry-Mieg, unpublished data and Ref. 25), and by systematically PCR-amplifying a cDNA library using...
Nature Reviews Genetics 2, 493 - 503 (01 Jul 2001) Review
12- Genome-wide detection of alternative splicing in
expressed sequences of human genes.
Modrek B, Resch A, Grasso C, Lee
C.
Nucleic Acids Res. 2001 Jul 1;
29(13): 2850-2859.
Abstract | Full Text | PDF-0.7M |
11- Bases and spaces: resources on the web
for accessing the draft human genome - II - After publication of the draft.
Genome Biol. 2001; 2(6):
reviews2001.1-reviews2001.6. published online before print June 5, 2001
Abstract | Full Text | PDF-0.5M |
10- Cloning,
expression, and characterization of a human inosine triphosphate
pyrophosphatase encoded by the itpa gene.
Lin S, McLennan AG, Ying K, Wang Z, Gu S, Jin H, Wu C, Liu W, Yuan Y, Tang R, Xie Y, Mao Y.
CONTEXT: Sequencing was performed on a PE-ABI 377 sequencer.
The Acembly program was used to assemble the full-length cDNA sequences. Vector
sequences were…
J Biol Chem. 2001 Jun 1;276(22):18695-701. Epub 2001 Mar 13.
9- Loss of Expression of Human Spectrin Src Homology Domain Binding Protein 1 is Associated with 10p Loss in Human Prostatic Adenocarcinoma
Jill A Macoska, Jiliu Xu, Dorota Ziemnicka, Tracy S Schwab, Mark A Rubin, Leszek Kotula
CONTEXT: ...The primer sequences were derived from Contig NT 008730 (GenBank) containing the entire Hssh3bp1 gene (see also AceView of the gene at NCBI web site at the address indicated above). Analysis of Hssh3bp1 Expression Frozen paired...
Neoplasia 3, 99 - 104 (11 May 2001) Original Article
8- Genomic structure
of the gene for mouse germ-cell nuclear factor (GCNF). II. Comparison with the
genomic structure of the human GCNF gene.
Susens U, Borgmeyer U.
CONTEXT: The AceView
analysis at the NCBI based on the draft sequence and a Blast search ...
Intron sizes given by the AceView analysis [ 26 ] were compared with the
...
Genome Biol. 2001; 2(5):
research0017.1-research0017.7. published online
before print May 2, 2001
Abstract | Full Text | PDF-89K |
7- Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans
Jérome Reboul, Philippe Vaglio, Nia Tzellas, Nicolas
Thierry-Mieg, Troy Moore, Cindy Jackson, Tadasu Shin-i, Yuji Kohara, Danielle
CONTEXT: ...sequenced. OST alignment. Alignment of OST sequences against the C. elegans genomic sequence was carried out using Acembly on version WS9 of ACeDB. Each OST sequence was aligned against the complete C. elegans genomic sequence to...
Nature Genetics 27, 332 - 336 (01 Mar 2001) Letters
6- Initial sequencing
and analysis of the human genome
Eric S. Lander, Lauren M. Linton, Bruce Birren, Chad Nusbaum, Michael C. Zody, Jennifer Baldwin, Keri Devon, Ken Dewar, Michael Doyle, William FitzHugh, Roel Funke, Diane Gage, Katrina Harris, Andrew Heaford, John Howland, Lisa Kann, ...
CONTEXT: ...genes were aligned with the draft genome sequence, using both the Spidey (S. Wheelan, personal communication) and Acembly (D. Thierry-Mieg and J. Thierry-Mieg, unpublished; http://www.acedb.org) computer programs. Because this...
Nature 409, 860 - 921 (15 Feb 2001) Human
5-
A candidate prostate cancer susceptibility gene at chromosome 17p
Sean V. Tavtigian, Jacques Simard, David H.F. Teng, Vicki Abtin, Michelle Baumgard, Audrey Beck, Nicola J. Camp, Arlene R. Carillo, Yang Chen, Priya Dayananth, Marc Desrochers, Martine Dumont, James M. Farnham, David Frank, Cheryl Frye, Siavash Ghaffari, Jamila S. Gupte, Rong Hu, Diana Iliev, Teresa Janecki, Edward N. Kort, Kirsten E. Laity, Amber Leavitt, Gilles Leblanc, Jodi McArthur-Morrison, Amy Pederson, Brandon Penn, Kelly T. Peterson, Julia E. Reid, Sam Richards, Marianne Schroeder, Richard Smith, Sarah C. Snyder, Brad Swedlund, Jeff Swensen, Alun Thomas, Martine Tranchant, Ann-Marie Woodland, Fernand Labrie, Mark H. Skolnick, Susan Neuhausen, Johanna Rommens, Lisa A. Cannon-Albright
CONTEXT: ...plasmid sublibraries generated from these clones. The sequence data obtained were assembled into contigs using Acembly, version 4.3 (U. Sauvage, D. Thierry-Mieg and J. Thierry-Mieg). Subsequently, a complete sequence of this interval...
Nature Genetics 27, 172 - 180 (01 Feb 2001) Article
4- Molecular cloning and characterization of a novel peptidylprolyl
isomerase (cyclophilin)-like gene (PPIL3) from human fetal brain.
Zhou Z, Ying K, Dai J, Tang R, Wang W, Huang Y, Zhao W, Xie Y, Mao Y.
CONTEXT: Assembly of all the
sequences from one clone was achieved with Acembly. The nucleotide sequences
reported
Cytogenet Cell Genet. 2001;92(3-4):231-6.
1 in 2000
3- JESAM: CORBA software components to create and publish EST
alignments and clusters.
Parsons JD,
Rodriguez-Tome P.
CONTEXT: describes
alignment algorithms in Acembly and compares then to other alignment software
Bioinformatics. 2000
Apr;16(4):313-25.
1 in 1999
2- Comparative Genomic Analysis of the
Interferon/Interleukin-10 Receptor Gene Cluster.
Reboul
J, Gardiner K, Monneron D, Uzé G, Lutfalla G.
CONTEXT: used Acembly to assemble and edit their sequences
Genome
Res. 1999 Mar; 9(3): 242-250.| PubLink |
1 in 1998
1- Distribution of
olfactory receptor genes in the human genome
Sylvie Rouquier,
Sylvie Taviaux, Barbara J. Trask, Véronique Brand-Arpon, Ger van den Engh,
Jacques Demaille, Dominique Giorgi
CONTEXT: ...were assembled for each clone and visually corrected from the electropherograms using the computer program Acembly version 4.3 (J. Thierry-Mieg and U. Sauvage, unpublished) built over the ACedb data manager (J. Thierry-Mieg ....
Nature Genetics 18, 243 - 250 (01 Mar 1998) Article