C-It: a knowledge database for tissue-enriched genes

C-It Help

C-It Help

Tip: Most sections in C-It are linked to short descriptions.

Just move your mouse over a dashed underlined text and a small window opens.

The functions of tens of thousands of genes in different species still remain unknown. “C-It” is a knowledge database which has its focus on “uncharacterized genes”. With C-It it is possible to screen for uncharacterized, tissue-enriched genes in Human, Mouse, Rat, Chicken and Zebrafish. Further expression studies are included to provide more comprehensive coverage of gene expression patterns and tissue-enriched splicing isoforms.

C-It offeres 3 different search methods:

Query by tissue

In the first step the tissue of interest has to be selected. C-It utilizes the EST profiles to identify tissue-enriched and depleted genes. Optionally a second tissue can be selected for a comparison (see next step).

The second step allows to search for enriched or depleted genes in the selected tissue(s). In this example, we selected heart and muscle in the previous step and are only interested in genes, that are enriched in heart, but not expressed in muscle. Further, up to four organism can be selected. Please note, that the availability is dependent on the selected tissues. C-It classifies "uncharacterized" genes as genes without/few publications. The default settings are fewer than 5 articles published per gene and fewer than 3 articles classified to the selected tissue(s) by MeSH.

The next pages shows the number of uncharacterized genes found in the selected organism. In our example heart enriched genes, which are not expressed in muscle, in Human, Mouse, Rat and Chicken are shown. This step allows to deselect organism, like we did here for Chicken, since only one gene was found in all four organism.

Dependent on the species and tissue, the last step provides the possibility to add further expression studies. In this example all available studies are shown. We selected SAGE libraries from Mouse Atlas of Gene Expression, SymAtlas and Exon Arrays from BioGPS and Affymetrix. Values of this studies will be integrated into the final table. In addition full gene names and PubMed IDs to each gene can be added.

The final table shows Homologene cluster and the according genes, including their expression information. In the case two tissues have been selected in the first step, some columns contain informations to both tissues, divided by a slash. More information about the columns is provided by clicking on "Help" in the gray row.
Gene IDs are linked directly to NCBI.

Each Homologene ID and number of publications found to the gene is linked to a table showing all homologs to this cluster in Human, Mouse, Rat, Chicken and Zebrafish. This view also shows the full gene name and all PubMed IDs the genes are mentioned in. Please note, that also large-scale articles are shown (articles mentioing more than 100 genes). These articles were excluded before classifying genes as "uncharacterized" and are shown in parenthesis.

The TPM column, as well as the additional expression informations are linked to diagrams showing the expression profile of the gene across all available tissues. They can also be accessed by just clicking on one of the tabs in the previous descriped view. The availability of the diagrams depends on the tissue and organisms.

If exon array data has been selected in the last step, a additional column shows the number of differentially expressed probe sets detected by exon arrays. This number is linked to a custom version of the Exon Arrays Analyzer. This allows to identify tissue-enriched alternative splice events. The Exon Array Analyzer has its own help page, which can be visited for detailed informations.

Query by single gene

To get a quick overview of the expression profile of a gene, this option can be used. The database can be queried by Entrez Gene or Symbol.

If more than one gene fits to the query, a certain gene has to be selected.

A click on a gene symbol will lead to the table showing all homologs in Human, Mouse, Rat, Chicken and Zebrafish (if available), as descriped above. The expression profile of the gene in all available tissues and expression studies is shown.

Query by list of genes

The third possibility to query C-It is to enter a list of Entrez Gene IDs. The species has to be selected in the dropdown box below.

Afterwards threshold for publications and the tissue of interest has to be selected.

C-It displays how many Entrez Gene IDs could be identified in the user supplied list and how many gene of them could pass the filter criteria.

The next steps are identical with the first query method. The user can add additional columns (expression studies, PubMed IDs and full gene names) and then a table with all genes is shown.