AmiGO Manual: Term Enrichment: Difference between revisions
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The Term Enrichment tool | The Term Enrichment tool can be used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms. The algorithm employed by the tool attempts to determine whether an observed level of annotation for a group of genes is significant within the context of annotation for all genes within the genome; examples of studies that have used this algorithm are [http://www.ncbi.nlm.nih.gov/pubmed/15492223 PMID:15492223] and [http://www.ncbi.nlm.nih.gov/pubmed/14561723 PMID:14561723]. AmiGO's Term Enrichment tool, which is based on the [http://search.cpan.org/dist/GO-TermFinder/ GO-TermFinder perl module by Gavin Sherlock and Shuai Weng] at Stanford University, allows users to specify a list of genes, define a background set against which the significance will be calculated and set the p-value (significance indicator) cut-off. | ||
Term enrichment is a very useful method for analyzing data from large scale experiments, such as gene clusters from microarray expression data. For a more detailed discussion of the algorithm, please see the [http://www.ncbi.nlm.nih.gov/pubmed/15297299 published material] on GO::TermFinder. | |||
Non-database filters (e.g. species, evidence code) are not used in the calculation. | Non-database filters (e.g. species, evidence code) are not used in the calculation. | ||
The input for the gene products may be either gene product symbols and/or ids separated by whitespace, or a file in the [http://www.geneontology.org/GO.format.annotation.shtml Gene Association File] format. | The input for the gene products may be either gene product symbols and/or ids separated by whitespace, or a file in the [http://www.geneontology.org/GO.format.annotation.shtml Gene Association File] format. | ||
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=Gene Product List= | =Gene Product List= | ||
... | The user may upload a whitespace separated list of gene product identifiers. These may be a mix of gene product symbols, synonyms or accessions. | ||
If the list is too large for manual input, the user may instead upload a either a file containing identifiers (as listed above) or a [http://www.geneontology.org/GO.format.annotation.shtml gene association file]. | |||
If AmiGO finds any gene product identifiers that are ambiguous or not found, the user will be informed before the end of the process. | |||
=Background Set= | =Background Set= | ||
. | The background set may input in a very similar way to the gene product list above. The only difference is the addition of an optional database filter. | ||
==Filtering== | ==Filtering== | ||
In summary, the must either enter/upload a background set, select a database filter, or do both. | |||
==Thresholds== | ==Thresholds== | ||
The | |||
please see the published materials for a detailed discussion of the | |||
=Advanced Options= | =Advanced Options= | ||
Revision as of 13:02, 10 March 2009
The Term Enrichment tool can be used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms. The algorithm employed by the tool attempts to determine whether an observed level of annotation for a group of genes is significant within the context of annotation for all genes within the genome; examples of studies that have used this algorithm are PMID:15492223 and PMID:14561723. AmiGO's Term Enrichment tool, which is based on the GO-TermFinder perl module by Gavin Sherlock and Shuai Weng at Stanford University, allows users to specify a list of genes, define a background set against which the significance will be calculated and set the p-value (significance indicator) cut-off.
Term enrichment is a very useful method for analyzing data from large scale experiments, such as gene clusters from microarray expression data. For a more detailed discussion of the algorithm, please see the published material on GO::TermFinder.
Non-database filters (e.g. species, evidence code) are not used in the calculation.
The input for the gene products may be either gene product symbols and/or ids separated by whitespace, or a file in the Gene Association File format.
Gene Product List
The user may upload a whitespace separated list of gene product identifiers. These may be a mix of gene product symbols, synonyms or accessions.
If the list is too large for manual input, the user may instead upload a either a file containing identifiers (as listed above) or a gene association file.
If AmiGO finds any gene product identifiers that are ambiguous or not found, the user will be informed before the end of the process.
Background Set
The background set may input in a very similar way to the gene product list above. The only difference is the addition of an optional database filter.
Filtering
In summary, the must either enter/upload a background set, select a database filter, or do both.
Thresholds
The
please see the published materials for a detailed discussion of the
Advanced Options
...
Result Types
...
Results Formats
...