Premium
Identification and functional analysis of essential, conserved, housekeeping and duplicated genes
Author(s) -
Arun P. V. Parvati Sai,
Miryala Sravan Kumar,
Chattopadhyay Subhayan,
Thiyyagura Kranthi,
Bawa Payal,
Bhattacharjee Madhuchhanda,
Yellaboina Sailu
Publication year - 2016
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.12192
Subject(s) - gene duplication , gene , biology , genome , housekeeping gene , genetics , computational biology , conserved sequence , gene expression , gene family , base sequence
Gene conservation, duplication and constitutive expression are intricately linked and strong predictors of essentiality. Here, we introduce metrics based on diversity indices to measure gene conservation, duplication and constitutive expression and validate them by measuring their performance in prediction of essential genes. Conservation and duplication were measured using the diversity indices on the bit score profile of Escherichia coli K12 orthologues, across the genomes, and paralogues, within the genome respectively. Constitutive expression was measured using expression diversity of E. coli K12 genes across different conditions. In addition, we developed a systematic method for enrichment analysis of gene‐sets in a given ranked list of genes. The method was used to identify genome‐wide functions of essential, conserved, constitutively expressed and duplicated genes. Furthermore, we also ranked various operons, complexes and pathways according to their essentiality, conservation, constitutive expression and duplication.