Gene Lists and Gene Details
Gene Lists
When you use the Gene Search, follow a gene number link from the Genome Details page, use the Phylogenetic Profiler, or view your Gene Cart, you will see a list of genes. All gene lists include checkboxes that can be used to add genes to your Gene Cart, and the list on the Gene Cart itself can be used to remove genes. Gene lists include the Object ID of the gene, its name, and the name of the genome in which it was found. These lists also show an EC number assignment for the gene's product, if one exists. You can click the gene Object ID to view the Gene Details page.
Gene Details
The Gene Details page includes information about the gene and provides options for examining this information. The Gene Information table includes gene identification information, locus information, chemical information about the product, and KEGG information. Each listed KEGG pathway is a link to the corresponding KEGG map. To see more information (gene description, whether the coordinates are wraparound coordinates, comments, product name, reaction, and scaffold source), click the "Show All Gene Information" button. To quickly run a BLASTp of the sequence against NR (NCBI's nonredundant protein database) click the "NCBI BLAST" button. This takes you to the BLAST page at the NCBI site.
Figure 23. Information about the gene is at the top of the Gene Details page
Evidence for Function Prediction
Below the Gene Information table is the Evidence for Function Prediction table (if there is one for this gene), including a graphic display of the gene's neighborhood (always shown); data from COG, InterPro, and Pfam; and lists of orthologs and paralogs.
Links in this display also provide access to the Chromosome Viewer and to neighborhood regions orthologous to the user-selected genomes.
To see all the homologs available in IMG (that is, showing both unidirectional and bidirectional hits), choose "All Homologs” in the Homolog selector pull-down list (beneath the Evidence for Function Prediction table). The other options are “Paralogs/Ortholog Clusters,” “Paralogs/Orthologs,” “Phenotype,” “Ecotype,” Disease,” and “Relevance.”
In the list of Ortholog Clusters and the list of Homologs, genes found in your selected genomes are highlighted in blue (if you have too many genomes selected, the highlighting is turned off since the purpose of highlighting is defeated when too many items are highlighted).
You can sort on linked column names for the Ortholog Cluster and Homolog tables to show most significant to least significant entries based on the column parameter.
Figure 24. Lists of paralogs and orthologs are provided below the Evidence for Function Prediction table
Viewing a Single Gene's Neighborhood
The Evidence for Function Prediction area of the Gene Details page provides a view of the gene's immediate neighborhood. The neighborhood is displayed graphically on a single line with the genes reading in one direction on top and those reading in the opposite direction on the bottom. The gene of interest is shown in red. Genes in the same positional cluster that are also in the same KEGG pathway are highlighted in green. When you move the cursor over any gene, you will see a popup box with the locus tag, gene name, and scaffold coordinates (except in Internet Explorer for the Macintosh). Click the arrow representing a gene to see the Gene Details page for that gene. To see more of the gene of interest's chromosome, click "Show in Chromosome Viewer." To see the neighborhoods of the gene and its orthologs, click "Show ortholog neighborhood regions in user-selected genomes."
Figure 25. Popup windows show details about a gene in the Gene Neighborhood
Viewing Neighborhoods for a Single Gene and its Orthologs
You can simultaneously view neighborhoods for the gene of interest and its orthologs in the genomes you have selected. You may want to avoid this option if you have all the genomes selected, since the page will be slow to load and the orthologs you would like to compare are not likely to be shown, because the number of displayed neighborhoods is limited. You can change the number of neighborhoods shown by entering a new setting for "Max. Taxon Gene Neighborhoods" on the Preferences page. The gene whose details you were viewing is shown in red at the center of the top neighborhood. Each ortholog is also shown in red in the center of its own neighborhood. Genes with the same color, except for the default light yellow, are from the same COG group. When you move the cursor over any gene, you will see a popup box with the locus tag, scaffold coordinates, and COG group number (except in Internet Explorer for the Macintosh). Click the arrow representing a gene to see the Gene Details page for that gene.
Figure 26. Viewing the neighborhoods of genes orthologous to the gene of interest
Using the Chromosome Viewer
The Chromosome Viewer shows all the genes in a range of sequence, with color coding by COG group. The gene whose details you were viewing is shown in red. If you move the cursor over a gene, you will see the gene name, COG code, and coordinates of that gene (except in Internet Explorer for the Macintosh). The COG code appears in brackets. Click an arrow to view details for the gene it represents.
Figure 27. Viewing a larger neighborhood with the Chromosome Viewer
The COG function coloring is customizable. By default, coloring is shown for all the COG groups. You can deselect as many as you want. If you deselect all of them, the coloring for all the groups will be turned on.
Viewing KEGG Pathway Maps
To view the KEGG map for a pathway that a particular gene is connected to, click the pathway name in the Gene Information table on the Gene Details page. If you don't see any pathways next to the "KEGG Pathway" heading, the gene has no KEGG pathway assignment.
Figure 28. Linking to the map for a KEGG pathway
Colored EC numbers on the KEGG map are links. Red links represent the current gene and point to the respective Gene Details page. Green links indicate genes in a positional cluster that includes the current gene, and these link to the Gene Details page for the positional cluster gene. Blue links are other genes identified in the same genome. Click a purple link to see a list of genes in the same genome with the same EC number. Orange links are "EC equivalogs," or genes found in other genomes that have the same EC number assignment. Click an orange link to view a list of those genes and a list of orthologs to those genes. Rounded rectangles are links to other pathway maps.
Figure 29. KEGG pathway maps have colored links to specific types of genes
Beneath the KEGG pathway map is a link to KEGG "Pathway Details." Refer to the "KEGG Pathway List and Details" section of this manual for more detail.
Viewing the Phylogenetic Distribution of Homologs
To view homologs for a particular gene, go to its Gene Details page and select "Phylogenetic Distribution." The phylogenetic list of genomes is displayed, with genomes containing a homolog of the gene of interest highlighted in red. The count of homologous genes at each level is shown in parentheses.
Figure 30. Viewing the phylogenetic distribution of homologs
Searching for Genes with Similar Phylogenetic Occurrence Profiles
In order to search for genes with similar phylogenetic occurrence profiles, you need to:
- Add the gene of interest to the Gene Cart, then go back to its Gene Details page by clicking on the “Gene Object ID” link in the Gene Cart.
- In the Gene Details page, click on the "Search Phylogenetic Profiles" button. Select the minimum percent occurrence match and number of results (“Top N results”) to be retrieved. The percent occurrence match determines the similarity threshold—the minimum required number of gene occurrence matches when comparing the profiles of two genes out of the total number of occurrences across all genomes.
- All genes with profiles that satisfy the minimum percent occurrence match condition are listed in descending percentage order. Select the genes of interest and add them to the Gene Cart.
- In the Gene Cart, select the genes of interest and click on the View Phylogenetic Occurrence Profiles button to display the profiles.
Figure 31. Searching for similar phylogenetic occurrence profiles
MyIMG Annotation
A user logged into IMG as individual "MyIMG" user may enter their own annotation directly into the gene details page. Generally, this functional annotation would be the intended "product name" for the gene. Other user annotations will also be visible on the gene details page. A gene may have multiple annotations from various users, but only one annotation per user is permitted for a given gene. The user's individual annotationa may be propagated through various selected paralogs, orthologs, or homologs by clicking on the "Save Annotation for Selections" button. For the logged in user, the user's own annotation, if present, is displayed in lieu of the original product name for various gene lists throughout the system for that user's session.
The MyIMG annotation option is only available through the "user restricted" site, a site requiring individual login. Additionally, a user may be restricted on genomes that are visible based on permission settings in the database. (The option is not available on the general public IMG site. If you are interested in doing annotation and need a user account, please request this through Questions / Comments link below.)
A user's annotation may be used to generate a Genbank or EMBL file, for example for viewing in Artemis, under the Export section of the Genome Details page. The user may optionally override the default product name of a gene with their own MyIMG annotation.