Searching for a program that does enrichment analysis from GO iD

Question

[ary.dantas161189]

Hi!

I have a transcriptome data from a spider in which we are trying to annotate the whole thing and do an enrichment analysis to find out what is the expression profile from this spider's venom gland. Since this spider (Loxosceles spp) has no reference genome on the NR-database, we are having a tough time annotating the whole transcriptome, we could only annotate 13k out of 62k (we do not have Blast2GO).

The transcriptome was obtained through an RNA-seq in an Illumina platform.

Thus, we used hmmer2go for that annotation and now we need a program to perform the enrichment analysis, do you have any sugggestion or know anything else we can use?

Here is an example of our input:

contig_35271_14 GO:0003743  GO:0031369  GO:0006413
contig_9403_9   GO:0016491  GO:0055114  GO:0016491
contig_54663_2  GO:0007165      
contig_8455_23  GO:0007218      
contig_380_34   GO:0005515  GO:0005089  GO:0035023
contig_4108_58  GO:0005515  GO:0005515  
contig_46052_10 GO:0005515  GO:0005515  
contig_5172_8   GO:0003676  GO:0004523

Thanks in advance!

Answer 1

[EagleEye]

Try GeneSCF v1.0 where you can input your own annotation file by following steps (below link),

A: GO enrichment analysis using a Text file with all the genes and GO ids associat

Orelse use GSEA preranked test

1) Convert your annotation file to GMT format.

2) Input your preranked gene/ID lists

Answer 2

[boczniak767]

You can also try ontologizer it is very flexible tool! You can provide your own annotation file (constructed following the GO specification - link). In fact it is also possible to use other than GO annotations (but it require building obo hierarchy) - eg. I've used to for InterPro domain enrichment.

The software is available as webstart java application (not always works due to java security settings) and command-line application. Makes nice graphs too!

[EagleEye]

From above example input, I do not think there is much information to construct GO association or hierarchy file (as I can see in requirements of Ontologizer). As I understood, the task is simple to use the above specified file as reference db file to perform enrichment analysis using different contig_xxxxx ids.

[boczniak767]

Since geneassociation file contains gene ID with corresponding GO categories (plus a bunch of columns which could be filled with, in fact, any data) it is possible. Construction of custom ontology is absolutely not required as it is generally universal. Take a look at row from my custom geneassociation for maize (it not precisely mirrors number of column because in some there are no data):

ensembl AC148152.3_FG006 AC148152.3_FG006 GO:0003824 NA|protein_coding|protein_coding IEA F catalytic activity AC148152.3_FGT006||| protein taxon:4577 160112 B73|AGPv2

[EagleEye]

This explains perfectly. Sorry, I guess I was wrong.