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 .05, 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 obo file: ../t/gene_ontology_edit.obo What is the aspect of this ontology you want to use (F, P, or C)? P Enter the fully qualified name of your associations file: ../t/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 37 -- GOID GO:0006790 TERM sulfur metabolism CORRECTED P-VALUE 1.47659150177758e-22 UNCORRECTED P-VALUE 3.99078784264211e-24 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 59 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET10, MET1, MET11, MET2, MET16, MET17 -- 2 of 37 -- GOID GO:0000096 TERM sulfur amino acid metabolism CORRECTED P-VALUE 4.5287552955708e-21 UNCORRECTED P-VALUE 1.22398791772184e-22 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 11 of 19 in the list, vs 32 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, MET17 -- 3 of 37 -- GOID GO:0006555 TERM methionine metabolism CORRECTED P-VALUE 1.70050438966192e-17 UNCORRECTED P-VALUE 4.59595780989708e-19 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 9 of 19 in the list, vs 23 of 7300 in the genome The genes annotated to this node are: MET14, MET1, MET11, MET3, STR3, MET2, MET16, MET17, MET6 -- 4 of 37 -- GOID GO:0006520 TERM amino acid metabolism CORRECTED P-VALUE 9.54842088570323e-16 UNCORRECTED P-VALUE 2.58065429343331e-17 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 184 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 5 of 37 -- GOID GO:0000097 TERM sulfur amino acid biosynthesis CORRECTED P-VALUE 1.01918487720888e-15 UNCORRECTED P-VALUE 2.75455372218618e-17 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 7 of 19 in the list, vs 10 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, MET28, MET17, MET6 -- 6 of 37 -- GOID GO:0006519 TERM amino acid and derivative metabolism CORRECTED P-VALUE 2.70276218187099e-15 UNCORRECTED P-VALUE 7.30476265370537e-17 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 199 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 7 of 37 -- GOID GO:0009308 TERM amine metabolism CORRECTED P-VALUE 1.14774161056767e-14 UNCORRECTED P-VALUE 3.10200435288561e-16 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 222 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 8 of 37 -- GOID GO:0009066 TERM aspartate family amino acid metabolism CORRECTED P-VALUE 1.79446311877879e-14 UNCORRECTED P-VALUE 4.84990032102375e-16 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 9 of 19 in the list, vs 45 of 7300 in the genome The genes annotated to this node are: MET14, MET1, MET11, MET3, STR3, MET2, MET16, MET17, MET6 -- 9 of 37 -- GOID GO:0006807 TERM nitrogen compound metabolism CORRECTED P-VALUE 3.77265283361447e-14 UNCORRECTED P-VALUE 1.01963590097688e-15 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 243 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 10 of 37 -- GOID GO:0044272 TERM sulfur compound biosynthesis CORRECTED P-VALUE 2.67188341651488e-13 UNCORRECTED P-VALUE 7.2213065311213e-15 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 7 of 19 in the list, vs 18 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, MET28, MET17, MET6 -- 11 of 37 -- GOID GO:0006082 TERM organic acid metabolism CORRECTED P-VALUE 7.06399274294626e-13 UNCORRECTED P-VALUE 1.90918722782331e-14 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 304 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 12 of 37 -- GOID GO:0019752 TERM carboxylic acid metabolism CORRECTED P-VALUE 7.06399274294626e-13 UNCORRECTED P-VALUE 1.90918722782331e-14 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 13 of 19 in the list, vs 304 of 7300 in the genome The genes annotated to this node are: MET14, MET3, STR3, ECM17, MET28, MHT1, MET6, MET1, MET11, MET2, MET16, YIL074C, MET17 -- 13 of 37 -- GOID GO:0000103 TERM sulfate assimilation CORRECTED P-VALUE 9.98928836937253e-13 UNCORRECTED P-VALUE 2.69980766739798e-14 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 6 of 19 in the list, vs 10 of 7300 in the genome The genes annotated to this node are: MET10, MET14, MET1, MET3, ECM17, MET16 -- 14 of 37 -- GOID GO:0006791 TERM sulfur utilization CORRECTED P-VALUE 9.98928836937253e-13 UNCORRECTED P-VALUE 2.69980766739798e-14 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 6 of 19 in the list, vs 10 of 7300 in the genome The genes annotated to this node are: MET10, MET14, MET1, MET3, ECM17, MET16 -- 15 of 37 -- GOID GO:0008652 TERM amino acid biosynthesis CORRECTED P-VALUE 4.728301511661e-11 UNCORRECTED P-VALUE 1.27791932747595e-12 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 9 of 19 in the list, vs 103 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, ECM17, YIL074C, MET28, MET17, MET6 -- 16 of 37 -- GOID GO:0009309 TERM amine biosynthesis CORRECTED P-VALUE 9.42530020402032e-11 UNCORRECTED P-VALUE 2.54737843351901e-12 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 9 of 19 in the list, vs 111 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, ECM17, YIL074C, MET28, MET17, MET6 -- 17 of 37 -- GOID GO:0044271 TERM nitrogen compound biosynthesis CORRECTED P-VALUE 9.42530020402032e-11 UNCORRECTED P-VALUE 2.54737843351901e-12 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 9 of 19 in the list, vs 111 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, ECM17, YIL074C, MET28, MET17, MET6 -- 18 of 37 -- GOID GO:0009086 TERM methionine biosynthesis CORRECTED P-VALUE 1.81352587001198e-08 UNCORRECTED P-VALUE 4.90142127030265e-10 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 4 of 19 in the list, vs 6 of 7300 in the genome The genes annotated to this node are: MET1, STR3, MET2, MET6 -- 19 of 37 -- GOID GO:0009067 TERM aspartate family amino acid biosynthesis CORRECTED P-VALUE 4.58690073266533e-06 UNCORRECTED P-VALUE 1.23970290072036e-07 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 4 of 19 in the list, vs 19 of 7300 in the genome The genes annotated to this node are: MET1, STR3, MET2, MET6 -- 20 of 37 -- GOID GO:0000101 TERM sulfur amino acid transport CORRECTED P-VALUE 5.51387718608536e-06 UNCORRECTED P-VALUE 1.49023707732037e-07 FDR_RATE 0.00% EXPECTED_FALSE_POSITIVES 0.00 NUM_ANNOTATIONS 3 of 19 in the list, vs 5 of 7300 in the genome The genes annotated to this node are: MMP1, MUP1, SAM3 -- 21 of 37 -- GOID GO:0009069 TERM serine family amino acid metabolism CORRECTED P-VALUE 0.00108164983836796 UNCORRECTED P-VALUE 2.92337794153502e-05 FDR_RATE 0.10% EXPECTED_FALSE_POSITIVES 0.02 NUM_ANNOTATIONS 3 of 19 in the list, vs 24 of 7300 in the genome The genes annotated to this node are: MET2, YIL074C, MET17 -- 22 of 37 -- GOID GO:0006865 TERM amino acid transport CORRECTED P-VALUE 0.00406448231248132 UNCORRECTED P-VALUE 0.000109850873310306 FDR_RATE 0.18% EXPECTED_FALSE_POSITIVES 0.04 NUM_ANNOTATIONS 3 of 19 in the list, vs 37 of 7300 in the genome The genes annotated to this node are: MMP1, MUP1, SAM3 -- 23 of 37 -- GOID GO:0044249 TERM cellular biosynthesis CORRECTED P-VALUE 0.00858173589265904 UNCORRECTED P-VALUE 0.000231938807909704 FDR_RATE 0.26% EXPECTED_FALSE_POSITIVES 0.06 NUM_ANNOTATIONS 9 of 19 in the list, vs 927 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, ECM17, YIL074C, MET28, MET17, MET6 -- 24 of 37 -- GOID GO:0015837 TERM amine transport CORRECTED P-VALUE 0.00888521048932255 UNCORRECTED P-VALUE 0.000240140824035745 FDR_RATE 0.33% EXPECTED_FALSE_POSITIVES 0.08 NUM_ANNOTATIONS 3 of 19 in the list, vs 48 of 7300 in the genome The genes annotated to this node are: MMP1, MUP1, SAM3 -- 25 of 37 -- GOID GO:0046942 TERM carboxylic acid transport CORRECTED P-VALUE 0.0100357228763322 UNCORRECTED P-VALUE 0.000271235753414384 FDR_RATE 0.40% EXPECTED_FALSE_POSITIVES 0.10 NUM_ANNOTATIONS 3 of 19 in the list, vs 50 of 7300 in the genome The genes annotated to this node are: MMP1, MUP1, SAM3 -- 26 of 37 -- GOID GO:0015849 TERM organic acid transport CORRECTED P-VALUE 0.0106454218366372 UNCORRECTED P-VALUE 0.000287714103692899 FDR_RATE 0.46% EXPECTED_FALSE_POSITIVES 0.12 NUM_ANNOTATIONS 3 of 19 in the list, vs 51 of 7300 in the genome The genes annotated to this node are: MMP1, MUP1, SAM3 -- 27 of 37 -- GOID GO:0009070 TERM serine family amino acid biosynthesis CORRECTED P-VALUE 0.0154325886116854 UNCORRECTED P-VALUE 0.000417096989505011 FDR_RATE 0.44% EXPECTED_FALSE_POSITIVES 0.12 NUM_ANNOTATIONS 2 of 19 in the list, vs 12 of 7300 in the genome The genes annotated to this node are: YIL074C, MET17 -- 28 of 37 -- GOID GO:0009058 TERM biosynthesis CORRECTED P-VALUE 0.0156316633253993 UNCORRECTED P-VALUE 0.000422477387172954 FDR_RATE 0.43% EXPECTED_FALSE_POSITIVES 0.12 NUM_ANNOTATIONS 9 of 19 in the list, vs 1002 of 7300 in the genome The genes annotated to this node are: MET1, MET11, STR3, MET2, ECM17, YIL074C, MET28, MET17, MET6
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.