Analysis of functional genomic signals using the XOR gate.

Full Abstract

Modeling gene regulatory networks requires recognition of active transcriptional sites in the genome. For this reason, we present a novel approach for inferring active transcriptional regulatory modules in a genome using an established systems model of bit encoded DNA sequences. Our analysis showed variations in several properties between random and functional sequences. Cross correlation within random and functional groups uncovered a wave pattern associated with functional sequences. Using the exclusive-OR (XOR) logic gate, we formulated a scheme to threshold signals that may correlate to putative active transcriptional modules from a population of random genomic fragments. It is our intent to use this as a basis for identifying novel regulatory sites in the genome.

Author information

Author/s: Yaragatti, Mahesh (M); Wen, Qi (Q);

Affiliation: Biotechnology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America. myar(-atsign-)seas.upenn.edu

Journal and publication information

Publication Type: Journal Article

Journal: PloS one (PLoS One), published in United States. (Language: eng)

Reference: 2009-; vol 4 (issue 5) : pp e5608

Dates: Created 2009/05/14; Completed 2009/08/06;

PMID: 19440336, status: MEDLINE (last retrieval date: 8/21/2009, IMS Date: )

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