GO enrichment analysis using a Text file with all the genes and GO ids associated for a non model organism

Question

[joynathan2]

I have the mapping of every gene in my organism to its GO id. Some genes doesn't have a GO id also. Below is an example of the format I have.

SeqName    length    score    eValue    hitName    GOs    ACC
Anisa00001    1185    656.751    0.0    gi|498338734|ref|WP_010652890.1|MULTISPECIES: integrase [Legionellaceae]      GO:0015074,GO:0006310,GO:0003677    WP_010652890.1,YP_006506632.1,CCD06721.1,ETO94118.1
Anisa00001    1185    466.463    6.16098E-161    gi|493924933|ref|WP_006869768.1|integrase [Legionella drancourtii]      GO:0015074,GO:0006310,GO:0003677    WP_006869768.1,EHL32123.1
Anisa00001    1185    424.861    1.43813E-144    gi|502743862|ref|WP_012978846.1|integrase [Legionella longbeachae]      GO:0015074,GO:0006310,GO:0003677    WP_012978846.1,YP_003454139.1,CBJ10990.1
Anisa00001    1185    423.705    4.53406E-144    gi|499535659|ref|WP_011216442.1|integrase [Legionella pneumophila]      GO:0015074,GO:0006310,GO:0003677    WP_011216442.1,YP_127815.1,CAH16726.1
Anisa00001    1185    419.468    2.18018E-142    gi|570283998|gb|AHE66185.1|site-specific recombinase XerD [Legionella oakridgensis ATCC 33761 = DSM 21215]      GO:0015074,GO:0006310,GO:0003677    AHE66185.1,ETO93999.1
Anisa00001    1185    413.69    4.08724E-140    gi|499526807|ref|WP_011213447.1|integrase [Legionella pneumophila]      GO:0015074,GO:0006310,GO:0003677    WP_011213447.1,YP_123415.1,CAH12239.1,ERB41210.1,ERH42153.1,ERI47405.1
Anisa00001    1185    413.69    6.12215E-140    gi|504092896|ref|WP_014326890.1|integrase [Legionella pneumophila]      GO:0015074,GO:0006310,GO:0003677    WP_014326890.1,YP_005185414.1,AEW51315.1
Anisa00001    1185    409.068    2.69005E-138    gi|499533894|ref|WP_011215175.1|integrase [Legionella pneumophila]      GO:0015074,GO:0006310,GO:0003677    WP_011215175.1,YP_126420.1,YP_006508280.1,CAH15303.1,CCD08390.1,KGP62973.1
Anisa00001    1185    404.831    1.16647E-136    gi|698843809|emb|CEG57778.1|Phage integrase family site-specific recombinase [Legionella fallonii LLAP-10]     GO:0015074,GO:0006310,GO:0003677    CEG57778.1
Anisa00003    297    176.022    7.21027E-56    gi|498338732|ref|WP_010652888.1|MULTISPECIES: hypothetical protein [Legionellaceae]      GO:0043565,GO:0003677    WP_010652888.1,YP_006506634.1,CCD06723.1,ETO94116.1
Anisa00003    297    120.168    9.08058E-34    gi|698843811|emb|CEG57780.1|conserved protein of unknown function [Legionella fallonii LLAP-10]     GO:0043565,GO:0003677    CEG57780.1
Anisa00003    297    93.9745    3.23067E-23    gi|493924102|ref|WP_006868999.1|hypothetical protein [Legionella drancourtii]      GO:0043565,GO:0003677    WP_006868999.1,EHL32770.1
Anisa00003    297    80.1073    5.8726E-18    gi|447092960|ref|WP_001170216.1|hypothetical protein [Leptospira interrogans]      GO:0043565,GO:0003677    WP_001170216.1,EMM81225.1
Anisa00003    297    78.1814    4.04598E-17    gi|489065186|ref|WP_002975201.1|DNA-binding helix-turn-helix protein [Leptospira terpstrae]      GO:0043565,GO:0003677    WP_002975201.1,EMY59958.1
Anisa00003    297    77.7962    5.73396E-17    gi|505585864|ref|WP_015678427.1|DNA-binding helix-turn-helix protein [Leptospira yanagawae]      GO:0043565,GO:0003677    WP_015678427.1,EOQ87907.1
Anisa00003    297    76.2554    2.31193E-16    gi|523642128|ref|WP_020778299.1|DNA-binding helix-turn-helix protein [Leptospira meyeri]      GO:0043565,GO:0003677    WP_020778299.1,EMJ85365.1
Anisa00003    297    75.8702    3.27591E-16    gi|489067540|ref|WP_002977532.1|DNA-binding helix-turn-helix protein [Leptospira vanthielii]      GO:0043565,GO:0003677    WP_002977532.1,EMY71198.1
Anisa00003    297    75.485    3.86738E-16    gi|490606321|ref|WP_004471330.1|MULTISPECIES: Cro/C1-type HTH DNA-binding domain protein [Leptospira]      GO:0043565,GO:0003677    WP_004471330.1,EKO33151.1,EKO78480.1,EMI68067.1,EMN22335.1,EMO21363.1
Anisa00003    297    75.8702    5.5926E-16    gi|488857175|ref|WP_002769485.1|hypothetical protein [Leptonema illini]      GO:0043565,GO:0003677    WP_002769485.1,EHQ05131.1
Anisa00003    297    75.0998    6.57594E-16    gi|501452877|ref|WP_012476326.1|hypothetical protein [Leptospira biflexa]      GO:0043565,GO:0003677    WP_012476326.1,YP_001963262.1,ABZ94684.1
Anisa00003    297    73.559    1.84265E-15    gi|685200322|gb|AIN94425.1|hypothetical protein JO40_10230 [Treponema putidum]     GO:0003677    AIN94425.1
Anisa00004    1233    466.463    1.24221E-160    gi|502743845|ref|WP_012978829.1|outer membrane-specific lipoprotein transporter subunit ; membrane component of ABC superfamily [Legionella longbeachae]      GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    WP_012978829.1,YP_003454078.1,CBJ10928.1
Anisa00004    1233    462.996    2.88424E-159    gi|698844250|emb|CEG58219.1|Lipoprotein-releasing system transmembrane protein LolC [Legionella fallonii LLAP-10]     GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    CEG58219.1
Anisa00004    1233    459.529    6.69725E-158    gi|570285197|gb|AHE67384.1|lipoprotein releasing system, transmembrane protein, LolC/E family [Legionella oakridgensis ATCC 33761 = DSM 21215]      GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    AHE67384.1,ETO93044.1
Anisa00004    1233    453.751    1.30772E-155    gi|504657357|ref|WP_014844459.1|outer membrane-specific lipoprotein ABC transporter permease [Legionella pneumophila]      GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    WP_014844459.1,YP_006509488.1,CCD09630.1
Anisa00004    1233    452.981    2.6206E-155    gi|506459505|ref|WP_015961405.1|hypothetical protein [Legionella pneumophila]      GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    WP_015961405.1,YP_124551.1,CAH13391.1,ERB41693.1,ERH43995.1,ERI49100.1
Anisa00004    1233    452.21    5.28713E-155    gi|499535375|ref|WP_011216187.1|hypothetical protein [Legionella pneumophila]      GO:0042954,GO:0042953,GO:0016021,GO:0016020,GO:0005886    WP_011216187.1,YP_127546.1,CAH16451.1

What I want to do is enrichment analysis for a subset of genes present in the above and see which GO terms are enriched in that subset of genes. Basically I am looking for Fisher's exact test or Hypergeometric Test. Is there any program that any one could suggest?

[Sam]

Do you have a text file or something that we can read, it is almost impossible to read the format here and it make things complicated

[Rama]

Hi,

You can use GO enrichment tool at PantherDB.org. Please check their paper in Nature Protocols (http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.092.html) on how to prepare the input file etc.

R

Answer 1

[EagleEye]

Four steps to go with GeneSCF: This will work with GeneSCF v1.0.

1) Tool:

• http://genescf.kandurilab.org/downloads.php
• Gene Set Clustering based on Functional annotation (GeneSCF)

2) Geneset database as textfile: https://github.com/santhilalsubhash/geneSCF/tree/master/geneSCF-master-v1.0/annotation

After making your annotation (DB) file in flat file format like these files. Put your file in annotation folder

3) Code to edit: https://github.com/santhilalsubhash/geneSCF/blob/master/geneSCF-master-v1.0/class/functional_class.pl

After line 103 add one more if condition for your database flat file: If you have only one type of GeneID, use only one IF condition.

if($ARGV[0] eq "gid" && $ARGV[3] eq "YOUR_DB_NAME")
{
$mytype="Entrez Gene ID";
open(IN1,"$ARGV[5]/annotation/YOUR_DB_FILE_withEntrezGeneID.txt") or die "Error opening in file";
}

if($ARGV[0] eq "sym" && $ARGV[3] eq "YOUR_DB_NAME")
{
$mytype="Gene Symbol";
open(IN1,"$ARGV[5]/annotation/YOUR_DB_FILE_withGeneSymbol.txt") or die "Error opening in file";
}

4) Now you can run GeneSCF

geneSCF -i=./your_listOfGenes_withgeneSym -db=YOUR_DB_NAME -o=./test/output -t=sym

[joynathan2]

Thanks. I made it work