termFinderClient.pl - interactive client to find significant GO terms for a list of genes
This program is a very simply client for the GO::TermFinder object, that prompts a user for the various pieces of information that are required to determine significant GO terms associated with the list of genes. It uses a p-value cut-off (for the corrected p-value) of .001, and simply prints the information back to the screen. An example below uses the genes : YPL250C, MET11, MXR1, MET17, SAM3, MET28, STR3, MMP1, MET1, YIL074C, MHT1, MET14, MET16, MET3, MET10, ECM17, MET2, MUP1 and MET6, which formed the so called methionine cluster from Spellman et al, 1998:
> termFinderClient.pl Enter the fully qualified name of your ontology file: process.ontology What is the aspect of this ontology (F, P, or C)? P Enter the fully qualified name of your associations file: gene_association.sgd Enter a the fully qualified name of your file with a list of genes for which to find term: genes.txt How many genes (roughly) exist within the organism? 7300 Finding terms... -- 1 of 28-- GOID GO:0006790 TERM sulfur metabolism P-VALUE 4.72498557073697e-25 CORRECTED P-VALUE 6.14248124195806e-24 NUM_ANNOTATIONS 13 (of 51) -- 2 of 28-- GOID GO:0000096 TERM sulfur amino acid metabolism P-VALUE 3.29201306923395e-23 CORRECTED P-VALUE 4.27961699000414e-22 NUM_ANNOTATIONS 11 (of 29) -- 3 of 28-- GOID GO:0006555 TERM methionine metabolism P-VALUE 9.48135258251747e-20 CORRECTED P-VALUE 1.23257583572727e-18 NUM_ANNOTATIONS 9 (of 20) -- 4 of 28-- GOID GO:0006520 TERM amino acid metabolism P-VALUE 1.06665546159811e-16 CORRECTED P-VALUE 1.38665210007754e-15 NUM_ANNOTATIONS 12 (of 145) -- 5 of 28-- GOID GO:0009066 TERM aspartate family amino acid metabolism P-VALUE 2.44942452266491e-16 CORRECTED P-VALUE 3.18425187946438e-15 NUM_ANNOTATIONS 9 (of 42) -- 6 of 28-- GOID GO:0006519 TERM amino acid and derivative metabolism P-VALUE 2.84201383187083e-16 CORRECTED P-VALUE 3.69461798143208e-15 NUM_ANNOTATIONS 12 (of 157) -- 7 of 28-- GOID GO:0009308 TERM amine metabolism P-VALUE 6.06713484278472e-16 CORRECTED P-VALUE 7.88727529562014e-15 NUM_ANNOTATIONS 12 (of 167) -- 8 of 28-- GOID GO:0000103 TERM sulfate assimilation P-VALUE 3.61076971610707e-15 CORRECTED P-VALUE 4.69400063093919e-14 NUM_ANNOTATIONS 6 (of 8) -- 9 of 28-- GOID GO:0006791 TERM sulfur utilization P-VALUE 3.61076971610707e-15 CORRECTED P-VALUE 4.69400063093919e-14 NUM_ANNOTATIONS 6 (of 8) -- 10 of 28-- GOID GO:0006082 TERM organic acid metabolism P-VALUE 2.41612157270023e-14 CORRECTED P-VALUE 3.1409580445103e-13 NUM_ANNOTATIONS 12 (of 226) -- 11 of 28-- GOID GO:0019752 TERM carboxylic acid metabolism P-VALUE 2.41612157270023e-14 CORRECTED P-VALUE 3.1409580445103e-13 NUM_ANNOTATIONS 12 (of 226) -- 12 of 28-- GOID GO:0000097 TERM sulfur amino acid biosynthesis P-VALUE 3.75638037739466e-12 CORRECTED P-VALUE 4.88329449061306e-11 NUM_ANNOTATIONS 5 (of 8) -- 13 of 28-- GOID GO:0008652 TERM amino acid biosynthesis P-VALUE 1.25659010245536e-07 CORRECTED P-VALUE 1.63356713319197e-06 NUM_ANNOTATIONS 6 (of 99) -- 14 of 28-- GOID GO:0000101 TERM sulfur amino acid transport P-VALUE 1.49023707732037e-07 CORRECTED P-VALUE 1.93730820051648e-06 NUM_ANNOTATIONS 3 (of 5) -- 15 of 28-- GOID GO:0009086 TERM methionine biosynthesis P-VALUE 1.49023707732037e-07 CORRECTED P-VALUE 1.93730820051648e-06 NUM_ANNOTATIONS 3 (of 5) -- 16 of 28-- GOID GO:0009309 TERM amine biosynthesis P-VALUE 1.89250974784783e-07 CORRECTED P-VALUE 2.46026267220218e-06 NUM_ANNOTATIONS 6 (of 106) -- 17 of 28-- GOID GO:0009067 TERM aspartate family amino acid biosynthesis P-VALUE 1.19029139172751e-05 CORRECTED P-VALUE 0.000154737880924577 NUM_ANNOTATIONS 3 (of 18) -- 18 of 28-- GOID GO:0006865 TERM amino acid transport P-VALUE 5.80646562760316e-05 CORRECTED P-VALUE 0.000754840531588411 NUM_ANNOTATIONS 3 (of 30)
Gavin Sherlock, sherlock@genome.stanford.edu
To install GO::TermFinder, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GO::TermFinder
CPAN shell
perl -MCPAN -e shell install GO::TermFinder
For more information on module installation, please visit the detailed CPAN module installation guide.