NDLI: On the Detection of Gene Network Interconnections using Directed Mutual Information

Content Provider	IEEE Xplore Digital Library
Author	Mathai, P. Martins, N.C. Shapiro, B.
Copyright Year	2007
Description	Author affiliation: Univ. of Maryland, College Park (Mathai, P.)
Abstract	In this paper, we suggest and validate a systematic method for inferring biological gene networks. So far, the identification of even a small portion of gene networks has been achieved by consensus over multiple cellular biology labs. A gene refers to the sequence of DNA that encodes a single protein. Proteins encoded by a gene can regulate other genes in the living cell, forming a complex network that determines cell growth, health, and disease. We view gene networks as dynamic systems, in discrete-time, formed by the interconnection among genes, which are abstracted as nodes whose state takes values in the range [-1, 1]. The state of each node is a function of the past values of the state of other nodes in the network. The edges of the gene network and their directions indicate functional dependence among the nodes state and their causality relationships, respectively. New engineering developments, such as quantum dot sensors, will allow measurement of gene dynamics inside living cells. From gene time-course data, we show how each edge in a gene network can be inferred using the concept of directed mutual information. We validated our method using small networks generated randomly, as well as for the known network for flagella biosynthesis in E.Coli, which we used to generate gene time-course data (with noise) in simulations. For acyclic graphs with 7 (or fewer) genes with summation operations only, we were able to infer all edges perfectly. We also present a heuristic method to deal with Boolean operations.
Starting Page	274
Ending Page	283
File Size	2520673
Page Count	10
File Format	PDF
ISBN	9780615153148
DOI	10.1109/ITA.2007.4357592
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-01-29
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	UCSD
Subject Keyword	Proteins Cellular networks Systematics Sequences DNA Cells (biology) Complex networks Biological information theory Mutual information Diseases
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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