NAME

termFinderClient.pl - interactive client to find significant GO terms for a list of genes

SYNOPSIS

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

AUTHORS

Gavin Sherlock, sherlock@genome.stanford.edu