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ProbCD: enrichment analysis accounting for categorization uncertainty

Ricardo Vêncio¹ & Ilya Shmulevich¹

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1. Institute for Systems Biology

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Document Type:

Manuscript

Date:

Received 06 July 2007 04:45 UTC; Posted 06 July 2007

Subjects:

Biotechnology, Genetics, Bioinformatics

Tags:

• contingency table
• gene ontology
• categorical data
• enrichment

Abstract:

As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for
the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.

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License:

This document is licensed to the public under the Creative Commons Attribution 2.5 License

How to cite this document:

Vêncio, Ricardo and Shmulevich, Ilya. ProbCD: enrichment analysis accounting for categorization uncertainty. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2007.369.1> (2007)

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Other versions of this document in Nature Precedings

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Other versions of this document elsewhere on the web

• http://arxiv.org/abs/0707.1503 :
• 10.1186/1471-2105-8-383 (Peer Reviewed):

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