Example Clients of GO::TermFinder and related modules

This directory contains various example client scripts that can be used to access the functionality of of the GO::TermFinder and related modules, that provide a rich API for accessing information from the Gene Ontology project. These examples serve the purpose of providing useful example code for people who wish to write alternate clients of these objects, as well as providing useful functionality in their own right.

Before running any of the example programs, you should first install the GO::TermFinder modules, according to the instructions in the README file. Also, see the associated pod for each example program for more information about that particular program.

The example client programs are:

1. analyze.pl

This program takes a list of files, each of which contain a list of genes, with one gene per line. It will findTerms for the lists of genes in each of the GO aspects, outputting the results to a file named for the original file, but with a .terms extension. It will only output terms with a corrected P-value of <= 0.05. It will use the first supplied argument as the annotation file, the second argument as the expected number of genes within the organism, and all subsequent files as ones containing lists of genes. You need to provide the ontology files in the same directory from which you are executing this script, and the GO-TermFinder libraries must be in your path.

Usage:

    analyze.pl <annotation_file> <numGenes> <file1> <file2> <file3> ... <fileN>

e.g.

    analyze.pl gene_association.sgd 7200 file1.txt file2.txt file3.txt

2. ancestors.pl

ancestors.pl simply takes as input a GOID, and an ontology file, and prints out the all the paths from that GO node to the root of the ontology, e.g:

    >ancestors.pl GO:0008346 ../t/process.ontology
    GO:0003673    Gene_Ontology
        GO:0008150    biological_process
            GO:0007610    behavior
                GO:0030537    larval behavior
                    GO:0008345    larval locomotory behavior
                        GO:0008346    larval walking behavior

    GO:0003673    Gene_Ontology
        GO:0008150    biological_process
            GO:0007610    behavior
                GO:0007626    locomotory behavior
                    GO:0008345    larval locomotory behavior
                        GO:0008346    larval walking behavior

3. batchGOView.pl

batchGoView.pl will read through a number of files, each containing a list of genes, and will create for each one an html page with a GO::View, such that you can graphically browse the results. You need to provide a .conf file, and then a list of files for processing, each of which contain a list of genes. An example .conf file exists in this directory - edit as appropriate. The following usage should give you some output, using the example files. Usage: batchGOView.pl <.conf_file>> <file1>> <file2> <file3> ... <fileN> e.g. batchGOView.pl GoView.conf genes.txt genes2.txt

Notes about the conf file:

The .conf file is simply a file that describes various parameters that can be used by batchGOView.pl. Each parameter is in the form of:

name = value

lines beginning with # are comment lines. See the example .conf file in the same directory as this html file.
Output from batchGOView.pl looks something like:

Terms for genes.txt

---



Result Table

Terms from the Process Ontology exceeding a pvalue cutoff of 1e-12

Gene Ontology term	Cluster frequency	Genome frequency of use	P-value	Genes annotated to the term
sulfur metabolism	13 out of 19 genes, 68.4%	45 out of 6905 genes, 0.7%	1.79e-24	STR3, MHT1, MET17, MET6, ECM17, MET1, MET2, MET3, MET16, MET28, MET11, MET14, MET10
sulfur amino acid metabolism	11 out of 19 genes, 57.9%	29 out of 6905 genes, 0.4%	7.27e-22	STR3, MHT1, MET17, MET6, MET1, MET2, MET3, MET16, MET28, MET11, MET14
methionine metabolism	9 out of 19 genes, 47.4%	20 out of 6905 genes, 0.3%	1.87e-18	STR3, MET17, MET6, MET1, MET2, MET3, MET16, MET11, MET14
aspartate family amino acid metabolism	9 out of 19 genes, 47.4%	41 out of 6905 genes, 0.6%	3.80e-15	STR3, MET17, MET6, MET1, MET2, MET3, MET16, MET11, MET14
sulfate assimilation	6 out of 19 genes, 31.6%	8 out of 6905 genes, 0.1%	6.04e-14	MET14, ECM17, MET1, MET3, MET16, MET10
sulfur utilization	6 out of 19 genes, 31.6%	8 out of 6905 genes, 0.1%	6.04e-14	MET14, ECM17, MET1, MET3, MET16, MET10
amino acid metabolism	11 out of 19 genes, 57.9%	141 out of 6905 genes, 2.0%	1.37e-13	STR3, MHT1, MET17, MET6, MET1, MET2, MET3, MET16, MET28, MET11, MET14
amino acid and derivative metabolism	11 out of 19 genes, 57.9%	151 out of 6905 genes, 2.2%	2.96e-13	STR3, MHT1, MET17, MET6, MET1, MET2, MET3, MET16, MET28, MET11, MET14
amine metabolism	11 out of 19 genes, 57.9%	161 out of 6905 genes, 2.3%	6.07e-13	STR3, MHT1, MET17, MET6, MET1, MET2, MET3, MET16, MET28, MET11, MET14

4. children.pl

children.pl simply takes as input a GOID, and an ontology file, and prints out the children of that GO node, e.g.:

    >children.pl GO:0008150 process.ontology

    Children of GO:0008150 (biological_process) : 

    GO:0000004    biological_process unknown
    GO:0016032    viral life cycle
    GO:0007582    physiological processes
    GO:0007275    development
    GO:0009987    cellular process
    GO:0008371    obsolete
    GO:0007610    behavior

5. termFinderClient.pl

   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.

Feedback on any and all of this software, clients or libraries alike, is welcomed and encouraged. We are more than happy to implement reasonable improvements and changes, and of course we always want to fix bugs. Please send feedback to Gavin Sherlock