CateGOrizer, previously known as "GO Terms Classifications Counter", is a free web
tool for users to batch analyze GO term data sets in terms of GO classes they
represent. One useful feature of
Gene Ontology (GO) is that it helps to describe the basic term hierarchies and
relationships between terms within the context of biology. It is usually a daunting
task to come up with a clear picture as how a set of GO terms are represented by
gene categories of GO. This web tool simplifies the process of database reasoning
by grouping and counting GO classes against a given classification methods such as
GO-Slim, taking advantage of pre-computed terms relationship based on the transitive
closure of GO database. This tool is comprised with a set of perl CGI programs
coupled with a MySQL DBMS that stores the GO terms DAG data.
Batch analysis of GO annotations for gene function groups is a useful part of
high-throughput microarray or EST data analysis.
This utility is for users to count the occurrences of their GO terms within each
of the pre-defined set of parent/ancestor GO terms. The program takes
GO terms (e.g. GO:0007067) in a list format or unformatted plain text file, perform
counts against one of the available classification methods
such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, etc. at user's choice, or against
one of your own classification methods, and then returns the results on the web
(if it takes too long, it will email the user with the results link).
The results include a table listing all counts and
percentages, along with a pie chart.
The use of the tool is as easy as following these three steps:
Step 1: Upload your GO id's
Step 2: Select a GO classification method
Step 3: Count occurrences of GO terms in each ancestral class
QUESTIONS AND ANSWERS:|
For proper use of this tool and related questions, see this list of
Frequently Asked Questions (FAQ). If you have any question
that's not covered by this FAQ, please don't hesitate to let us know.
All feedbacks on problems and suggestions to improve the tool are appreciated.
, Jie Bao and James M. Reecy (2007).
"A Gene Ontology (GO) Terms Classifications Counter".
Plant & Animal Genome XV Conference, San Diego, CA, January 13-17, 2007.