| Version 3.218 May 06, 2010 |
CateGOrizer, previously known as "GO Terms Classifications Counter", is an improved 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 categorizing 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.
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INTRODUCTION: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 find out the occurrences of their GO terms within each of the pre-defined set of parent/ancestor GO terms. The program takes input of GO terms (e.g. GO:0007067) in a list format or unformatted plain text file, perform step-wise classification against one of the available GO slim methods such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, etc. at user's choice, r 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 final counts and percentages, along with a pie chart. | |
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USAGES:
The use of the tool is as easy as following these three steps: Step 1: Upload your GO id'sStep 2: Select a GO classification methodStep 3: Count occurrences of GO terms in each ancestral class | |
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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. | |
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PUBLICATIONS:
Zhi-Liang Hu, Jie Bao and James M. Reecy (2008) "CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories". Online Journal of Bioinformatics. 9 (2):108-112.
Zhi-Liang Hu, 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.
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Google citations: 263 by 2023