Gene Ontology analysis from and heterogeneous list of genes names

Question

[friasoler]

Hello everybody!!! I need help to find a tool to make the GO for a list of genes from swissprot ...the name of the genes came from different organisms and I cant find the way to make a network or list of function related with this list of genes...

My best regards
Roberto

EDIT:

This is an example:

IBP2_CHICK
LEG3_CANFA
ACOD_CYPCA
H0ZCD8_TAEGU
NRK2_HUMAN
OMD_HUMAN
SIAT1_HUMAN
DPP10_MOUSE
BCL6_HUMAN
H0Z702_TAEGU
COCA1_HUMAN
HIAT1_HUMAN
COCA1_HUMAN
FAAH1_PIG
CADM1_MOUSE
LYOX_CHICK
HIAT1_HUMAN
H0Z4R0_TAEGU
ITIH5_HUMAN
GNTK_MOUSE
KAD3_BOVIN

CO7_PIG
HRSL3_PONAB
PKDCC_MOUSE
MPP7_DANRE
COL10_HUMAN
CAD13_HUMAN
SEM3C_CHICK
OTUL_MOUSE
CAD13_CHICK
G3UTX4_MELGA
LIN7A_MOUSE
OTUL_MOUSE
CDC42_CANAW
LRC8D_MOUSE
POK5_HUMAN
PRS35_HUMAN
KIF1A_MOUSE
FRK_MOUSE
APOA1_CHICK
QSOX1_CHICK
SEM3C_MOUSE

Answer 1

[TriS]

try DAVID (http://david.abcc.ncifcrf.gov/summary.jsp). it will show you the specie specific functional enrichments...including GO terms.

I'm not sure it takes swiss prot as inputs but you can convert your IDs using biomart (http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2)

[friasoler]

Oh thanks I have tried both....and I can't convert all IDs and David is so complicated to get the ontology ....I'm using Cytoscape(ClueGO and BIngo), Biomart David Gorila.....Genemania ....I'm really stressed with this. I need a tool to homogenize all this names in one format .....Thanks Thanks

[TriS]

OK, one thing first, unless you have a full answer use the "add a comment" section, this will help visually.

Now, clueGO might even be more complicated than David to use since it has lots of parameters that can be confusing unless you know what they are. another easy-to-use tool is amiGO.

Looks like you have gene names, so you don't need conversion.

What I would do are two things:

Unless you are familiar with R or Unix, paste your list of genes in Excel and do the following:

1. Paste or open the file with the list of genes in Excel
2. Go to Data -> text to columns (under tools) -> in "delimiters" select "others" and put "_" (with NO quotes), this will divide your gene name and species
3. Sort by species
4. Go to David (link above)
5. Create one list per each species
   1. Select "upload" from the left frame
   2. Paste your list of genes
   3. In "step 2" select "official gene names"
   4. Select "gene list" from "step 3"
   5. Click submit
   6. A Gene List Manager opens up
   7. Select your species from the list and click "use"
   8. Rename the list of genes with the name of the species
6. if you click on "gene ontology" you will see the GO analysis, click on "chart" and it will show you the results

Let us know if this helps

[friasoler]

Thanks! I will try this, hope I can get something thank you very much! I'll comment later what I got

regards

roberto

Answer 2

[Mo]

Did you check this function in R?

http://www.bioconductor.org/packages/release/data/annotation/html/GO.db.html