Inferring connectivity of genetic regulatory networks using information-theoretic criteria

Wentao Zhao, Erchin Serpedin, Edward R. Dougherty

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

Recently, the concept of mutual information has been proposed for infering the structure of genetic regulatory networks from gene expression profiling. After analyzing the limitations of mutual information in inferring the gene-to-gene interactions, this paper introduces the concept of conditional mutual information and based on it proposes two novel algorithms to infer the connectivity structure of genetic regulatory networks. One of the proposed algorithms exhibits a better accuracy while the other algorithm excels in simplicity and flexibility. By exploiting the mutual information and conditional mutual information, a practical metric is also proposed to assess the likeliness of direct connectivity between genes. This novel metric resolves a common limitation associated with the current inference algorithms, namely the situations where the gene connectivity is established in terms of the dichotomy of being either connected or disconnected. Based on the data sets generated by synthetic networks, the performance of the proposed algorithms is compared favorably relative to existing state-of-the-art schemes. The proposed algorithms are also applied on realistic biological measurements, such as the cutaneous melanoma data set, and biological meaningful results are inferred.

Original languageEnglish
Article number4359862
Pages (from-to)262-273
Number of pages12
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume5
Issue number2
DOIs
Publication statusPublished - Apr 2008
Externally publishedYes

Fingerprint

Genetic Regulatory Networks
Information Services
Mutual Information
Connectivity
Genes
Gene
Genetic Structures
Metric
Melanoma
Excel
gene interaction
genes
Gene Expression Profiling
Dichotomy
melanoma
Profiling
Gene expression
Gene Expression
gene regulatory networks
Resolve

Keywords

  • Biology and genetics
  • DNA microarray
  • Genetic regulatory network
  • Information theory

ASJC Scopus subject areas

  • Engineering(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Inferring connectivity of genetic regulatory networks using information-theoretic criteria. / Zhao, Wentao; Serpedin, Erchin; Dougherty, Edward R.

In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, 4359862, 04.2008, p. 262-273.

Research output: Contribution to journalArticle

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