title: Identification and functional analysis of essential, conserved, housekeeping and duplicated genes.
abstract: 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.
authors.affiliation: CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.
authors.forename: P V Parvati Sai
authors.initials: PV
authors.lastname: Arun
authors.affiliation: CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.|National Institute of Animal Biotechnology, Hyderabad, Telangana, India.
authors.forename: Sravan Kumar
authors.initials: SK
authors.lastname: Miryala
authors.affiliation: School of Mathematics and Statistics, University of Hyderabad, Hyderabad, Telangana, India.
authors.forename: Subhayan
authors.initials: S
authors.lastname: Chattopadhyay
authors.affiliation: CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.
authors.forename: Kranthi
authors.initials: K
authors.lastname: Thiyyagura
authors.affiliation: CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.
authors.forename: Payal
authors.initials: P
authors.lastname: Bawa
authors.affiliation: School of Mathematics and Statistics, University of Hyderabad, Hyderabad, Telangana, India.
authors.forename: Madhuchhanda
authors.initials: M
authors.lastname: Bhattacharjee
authors.affiliation: CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.
authors.forename: Sailu
authors.initials: S
authors.lastname: Yellaboina
mesh_terms: D019295:Computational Biology; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D020043:Genes, Essential; D053858:Metabolic Networks and Pathways; D009876:Operon; D012372:ROC Curve
chemical_list: D029968:Escherichia coli Proteins
keywords: conservation; duplication, essential and diversity indices