Help with Gene Groups Database

Poster

Here's a poster (pdf) describing this database.

Input

Input format can be comma or whitespace (tabs, newlines, spaces) delimited lists of genes. (Batch upload is now available).

Gene Names

Currently there are no restrictions on what type of gene identifiers you enter. Genes currently in the database were added from Gene Ontology and L2L, and I just used the gene names they used.

Output

Output can be in any of the following formats:

gene1     group1
gene2     group1
gene3     group2
gene4     group2

group1     gene1     gene2
group2     gene3     gene4

group_name      description     gene_name       gene_name       gene_name
group_name      description     gene_name       gene_name       gene_name

These formats were chosen based on iGA, CatMap, and GSEA's required inputs.

Tags

Gene groups, upon entry, can be tagged as belonging to various categories (e.g. yeast, meiosis) to make later access easier. Tags are also shown in a "tag cloud" where the font size is determined by the number of groups tagged by that term. For more information on tags, see wikipedia, flickr, or delicious.

Using iGA

1. Download iGA and the iGA manual.
2. Create a list of (gene tab ratio) in descending order by expression values (like a log ratio). Comment lines can start with #. Example:
```
#gene	#log2(Mut/WT)
rad24	3.99875
msh6	1.8242
sib1	1.5760
...
```
3. Right click here and select "Save as" or "Save link as" to download all gene groups in iGA appropriate format from this website.
4. Open up the command prompt, move to the directory you saved iGA into (cd C:/Documents/iGA or something), and call the program like this:
```
1471-2105-5-34-S1.exe -Iratios.txt -Agroups_iGA.txt
```
where ratios.txt is your genes and ratios file and groups_iGA.txt is your gene groups file.
5. View output - tells the groups, p-values, and percent changed. Read the manual for more information.

Using Catmap

2. Download Catmap.
3. Right click here and select "Save as" or "Save link as" to download all gene groups in Catmap format from gene groups database.
4. Get a list of genes in rank order by some metric, put in a gene tab gene tab gene format list. (all on one line). Call this genes.txt.
5. Create a "Settings" file in the following format (tab-delimited, you can use excel, then save as text) and save as settings.txt:
```
#Settings for Catmap.pl
categoryfile	groups_Catmap.txt
listfile	genes.txt
randomnull
outputfile	output.txt
companionfile	companion.txt
```
where groups_Catmap.txt is the gene groups file you download from this website, genes.txt is a list of genes in the format gene tab gene tab gene (all on one line). The output.txt file is where the output will go, and companion.txt is where additional output will go. Read the included README file for more information.
4. Run Catmap using
```
perl Catmap.pl -s settings.txt
```
5. Check output.txt and companion.txt for the output. Output should include a list of groups with p-values, percentiles, etc.

Using GSEA

GSEA

Using limma geneSetTest

The R bioconductor package limma also has a geneSetTest() command. This may be the best one yet. To use geneSetTest, you should probably have some familiarity with R and limma. Then check the limma user's guide. I might put a working example up here at some point. Feel free to contact me if you have questions.

gene groups database