title: In-silico gene co-expression network analysis in Paracoccidioides brasiliensis with reference to haloacid dehalogenase superfamily hydrolase gene.
abstract: BACKGROUND
  Paracoccidioides brasiliensis, a dimorphic fungus is the causative agent of paracoccidioidomycosis, a disease globally affecting millions of people. The haloacid dehalogenase (HAD) superfamily hydrolases enzyme in the fungi, in particular, is known to be responsible in the pathogenesis by adhering to the tissue. Hence, identification of novel drug targets is essential.
  
  
  OBJECTIVE
  In-silico based identification of co-expressed genes along with HAD superfamily hydrolase in P. brasiliensis during the morphogenesis from mycelium to yeast to identify possible genes as drug targets.
  
  
  METHODS
  In total, four datasets were retrieved from the NCBI-gene expression omnibus (GEO) database, each containing 4340 genes, followed by gene filtration expression of the data set. Further co-expression (CE) study was performed individually and then a combination these genes were visualized in the Cytoscape 2. 8.3.
  
  
  METHODS
  Mean and standard deviation value of the HAD superfamily hydrolase gene was obtained from the expression data and this value was subsequently used for the CE calculation purpose by selecting specific correlation power and filtering threshold.
  
  
  RESULTS
  The 23 genes that were thus obtained are common with respect to the HAD superfamily hydrolase gene. A significant network was selected from the Cytoscape network visualization that contains total 7 genes out of which 5 genes, which do not have significant protein hits, obtained from gene annotation of the expressed sequence tags by BLAST X. For all the protein PSI-BLAST was performed against human genome to find the homology.
  
  
  CONCLUSIONS
  The gene co-expression network was obtained with respect to HAD superfamily dehalogenase gene in P. Brasiliensis.
authors.affiliation: School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha, India.
authors.forename: Raghunath
authors.initials: R
authors.lastname: Satpathy
authors.affiliation: School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India.
authors.forename: V B
authors.initials: VB
authors.lastname: Konkimalla
authors.affiliation: School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha, India.
authors.forename: Jagnyeswar
authors.initials: J
authors.lastname: Ratha
keywords: Dimorphic fungi; drug target; gene annotation; gene co-expression network; microarray analysis