Overview

• The GeneDecks project aims to enhance the querying options of the GeneCards database. While GeneCards displays information for each gene separately, GeneDecks offers views and analyses about gene sets.

• The first stage of GeneDecks concentrates on gene similarity through their attributes. A gene attribute is any information field in GeneCards, e.g. its protein domains, the pathways it participates in, or its sequence. GeneDecks provides sets of genes similar to a gene of interest with respect to the selected attribute.

• Currently you can use GeneDecks through the GeneDecks homepage to view sets of similar genes for a list of sample genes, or by clicking on the GeneDecks icon in various sections of a gene's displayed card. GeneDecks is now available for the pathways, domains, and tissue expression attributes. For example, when viewing the Domains section of the card for your gene of interest, you can choose one or more of the protein domains as GeneDecksing candidates. After selecting the relevant domains and clicking on the GeneDecks icon, you receive a results page that includes: an explanatory title, a summary table and detail tables.

• We plan to provide GeneDecks for more attributes in GeneCards, as well as to improve the usefulness of its output by enabling submission of the found gene set symbols to our GeneALaCart batch query mechanism.

• The next stage of GeneDecks, currently in progress, includes annotation enrichment analysis based on GeneCards annotations.

• Future research and development will concentrate on increasing the flexibility and range of analyses on GeneCards data along planned improvements of the database.

   The Title

• The title lines list the selected descriptors for the genedecksed gene, in 2 legible columns.

   The Summary Table

• The summary table lists all existing combinations of selected descriptors and the genes associated with each such combination. Each link has a tool-tip for clarity. The number of items in each list appears in the preceding column. The names of descriptors are sorted by length, for easy reading. The names of genes are sorted alphanumerically, for easy searching. The background for each group of descriptors lists is distinctly marked in alternating colors
• The summary table now ranks the degree of similarity between the identified genes and the probe gene, taking into consideration all shared combinations of annotations. Thus, if a particular probe gene has N annotations in a given category (e.g. is involved in N pathways or has N domains), GeneDecks separately depicts sets of genes associated with any combination of M of the annotations, 1

   

Legend:

1. "About this table" link: an easy link to this page, placed above and below the table, for your convenience
2. Commonality count (pathway) column: the number of descriptors in this combination, out of the total descriptor count
3. Small card-deck logo (pathways names column): a clickable GeneDecks logo, linked to the full list of genes sharing this combination of descriptors
4. Descriptor name link (pathways names column): a clickable logo to the home page of the descriptor whose name follows
5. Gene name link (gene names column): a clickable name of participating genes, each linked to its GeneCard
6. "see all #" link: when more than 5 genes are associated with one combination of descriptors, only 5 are shown by default, with a link to the full list

   The Details Table

• The set of genes associated with each chosen domain. For each gene, the GeneCards description and the GeneCards identifier (GC IDs) are shown.