AmiGO Manual: Slimmer: Difference between revisions
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=Overview= | |||
The Slimmer tool allows you to map the granular annotations of the query set of genes to one or more high-level, broader parent terms referred to as GO Slim terms. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent (ie. GO slim) terms. The Slimmer tool can be useful in reporting the results of GO annotations of a genome, analyzing the results of microarray expression data, or cDNA collection using a high level view of the three ontologies. | The Slimmer tool allows you to map the granular annotations of the query set of genes to one or more high-level, broader parent terms referred to as GO Slim terms. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent (ie. GO slim) terms. The Slimmer tool can be useful in reporting the results of GO annotations of a genome, analyzing the results of microarray expression data, or cDNA collection using a high level view of the three ontologies. | ||
=Gene Product List= | =Usage= | ||
==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. | |||
===Filtering=== | |||
If the user selects a database filter, the inputted gene product list (or gene association file) will be filtered so that only gene products that are found in that database will be used in the calculations. This can help to remove a lot of possible ambiguity in the inputted set. | |||
The user may also select to filter by [http://www.geneontology.org/GO.evidence.shtml evidence code], which will | |||
==Slim Terms== | |||
GO IDs should be entered in the form: "GO:nnnnnnn", where 'n' is an integer. | |||
Please remember that if you are uploading an OBO file | |||
==Advanced Options== | |||
Clicking on '''Display advanced result options''' gives advanced users access to additional settings. | |||
===Result Types=== | |||
In addition to the '''standard results''' that are returned from this page, the user may also select '''all results''', which will return all results without any kind of threshold filtering (and ignoring any threshold inputs specified above). | |||
The '''gene product counts''' option is the default result and what most people find useful. | |||
The '''gene association file''' option does pretty much what you'd expect and generates a [http://www.geneontology.org/GO.format.annotation.shtml gene association file] view of the results. | |||
... | The '''mapping file''' option generates a mapping file of the results as described in the [http://search.cpan.org/~cmungall/go-perl/scripts/map2slim map2slim documentation]. | ||
The '''mapping file fo every term''' option is the same as above except that it covers the whole ontology and not just the inputted subset. Be aware that this option generates a large file and is very resource intensive--please use with caution. | |||
===Result Formats=== | |||
In addition to the standard '''html page''' results, the user may instead select a '''tab-delimited file''' or an '''xml file'''. Please be warned that the XML file is in an unstable internal format and should only really be used by people prefer parsing XML over other types. | |||
[[Category:AmiGO_Manual]] | [[Category:AmiGO_Manual]] | ||
[[Category:AmiGO]] | [[Category:AmiGO]] | ||
Revision as of 13:46, 10 March 2009
Overview
The Slimmer tool allows you to map the granular annotations of the query set of genes to one or more high-level, broader parent terms referred to as GO Slim terms. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent (ie. GO slim) terms. The Slimmer tool can be useful in reporting the results of GO annotations of a genome, analyzing the results of microarray expression data, or cDNA collection using a high level view of the three ontologies.
Usage
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.
Filtering
If the user selects a database filter, the inputted gene product list (or gene association file) will be filtered so that only gene products that are found in that database will be used in the calculations. This can help to remove a lot of possible ambiguity in the inputted set.
The user may also select to filter by evidence code, which will
Slim Terms
GO IDs should be entered in the form: "GO:nnnnnnn", where 'n' is an integer.
Please remember that if you are uploading an OBO file
Advanced Options
Clicking on Display advanced result options gives advanced users access to additional settings.
Result Types
In addition to the standard results that are returned from this page, the user may also select all results, which will return all results without any kind of threshold filtering (and ignoring any threshold inputs specified above).
The gene product counts option is the default result and what most people find useful.
The gene association file option does pretty much what you'd expect and generates a gene association file view of the results.
The mapping file option generates a mapping file of the results as described in the map2slim documentation.
The mapping file fo every term option is the same as above except that it covers the whole ontology and not just the inputted subset. Be aware that this option generates a large file and is very resource intensive--please use with caution.
Result Formats
In addition to the standard html page results, the user may instead select a tab-delimited file or an xml file. Please be warned that the XML file is in an unstable internal format and should only really be used by people prefer parsing XML over other types.