Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families.

Nucleic Acids Research
Larry N Singh, Sridhar Hannenhalli

Abstract

Gene duplication is integral to evolution, providing novel opportunities for organisms to diversify in function. One fundamental pathway of functional diversification among initially redundant gene copies, or paralogs, is via alterations in their expression patterns. Although the mechanisms underlying expression divergence are not completely understood, transcription factor binding sites and nucleosome occupancy are known to play a significant role in the process. Previous attempts to detect genomic variations mediating expression divergence in orthologs have had limited success for two primary reasons. First, it is inherently challenging to compare expressions among orthologs due to variable trans-acting effects and second, previous studies have quantified expression divergence in terms of an overall similarity of expression profiles across multiple samples, thereby obscuring condition-specific expression changes. Moreover, the inherently inter-correlated expressions among homologs present statistical challenges, not adequately addressed in many previous studies. Using rigorous statistical tests, here we characterize the relationship between cis element divergence and condition-specific expression divergence among paralogous g...Continue Reading

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Citations

Dec 6, 2011·Nucleic Acids Research·Aaron T Spivak, Gary D Stormo
Nov 19, 2013·BMC Systems Biology·Julio A Freyre-GonzálezRosa-María Gutiérrez-Ríos
Nov 15, 2014·BMC Systems Biology·Christopher L PlaisierNitin S Baliga
Mar 13, 2012·Biochimica Et Biophysica Acta·Maria Katherine Mejia-GuerraErich Grotewold
Jul 2, 2010·Current Opinion in Genetics & Development·Klaus H Kaestner

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Datasets Mentioned

BETA
GPL90
GSM29914

Methods Mentioned

BETA
ChIP-chip
ChIP

Software Mentioned

_ SCAN
Bioconductor
PWM
Affymetrix
SCAN
car R
Ensembl

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