title: Disease specific modules and hub genes for intervention strategies: A co-expression network based approach for Plasmodium falciparum clinical isolates.
abstract: Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, approaches that can provide information about the biological processes that are active in this parasite in vivo during complicated malaria conditions have been scarcely deployed. Here we report the analysis of a weighted gene co-expression based network for P. falciparum, from non-cerebral clinical complications. Gene expression profiles of 20 P. falciparum clinical isolates were utilized to construct the same. A total of 20 highly interacting modules were identified post network creation. In 12 of these modules, at least 10% of the member genes, were found to be differentially regulated in parasites from patient isolates showing complications, when compared with those from patients with uncomplicated disease. Enrichment analysis helped identify biological processes like oxidation-reduction, electron transport chain, protein synthesis, ubiquitin dependent catabolic processes, RNA binding and purine nucleotide metabolic processes as associated with these modules. Additionally, for each module, highly connected hub genes were identified. Detailed functional analysis of many of these, which have known annotated functions underline their importance in parasite development and survival. This suggests, that other hub genes with unknown functions may also be playing crucial roles in parasite biology, and, are potential candidates for intervention strategies.
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: amit4help@gmail.com.
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Subudhi
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: boopathiarunachalam@gmail.com.
authors.forename: Pon Arunachalam
authors.initials: PA
authors.lastname: Boopathi
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: aahana10123@gmail.com.
authors.forename: Isha
authors.initials: I
authors.lastname: Pandey
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: ramanme24@gmail.com.
authors.forename: Ramandeep
authors.initials: R
authors.lastname: Kaur
authors.affiliation: Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India. Electronic address: Sheetumig21@gmail.com.
authors.forename: Sheetal
authors.initials: S
authors.lastname: Middha
authors.affiliation: Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India. Electronic address: Jyotiacharya2@gmail.com.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Acharya
authors.affiliation: Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India. Electronic address: drskkochar@rediffmail.com.
authors.forename: Sanjay K
authors.initials: SK
authors.lastname: Kochar
authors.affiliation: Rajasthan University of Health Sciences, Jaipur, Rajasthan, India. Electronic address: drdkkochar@yahoo.com.
authors.forename: Dhanpat K
authors.initials: DK
authors.lastname: Kochar
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India. Electronic address: ashisd28@gmail.com.
authors.forename: Ashis
authors.initials: A
authors.lastname: Das
mesh_terms: D019295:Computational Biology / Q000379:methods; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D016778:Malaria, Falciparum / Q000150:complications* / Q000469:parasitology; D020411:Oligonucleotide Array Sequence Analysis; D010963:Plasmodium falciparum / Q000235:genetics* / Q000302:isolation & purification*; D015800:Protozoan Proteins / Q000235:genetics*
chemical_list: D015800:Protozoan Proteins
keywords: Complicated malaria; Plasmodium falciparum; Weighted gene co-expression network