No3CoGP: non-conserved and conserved coexpressed gene pairs View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-12

AUTHORS

Chittabrata Mal, Md Aftabuddin, Sudip Kundu

ABSTRACT

BACKGROUND: Analyzing the microarray data of different conditions, one can identify the conserved and condition-specific genes and gene modules, and thus can infer the underlying cellular activities. All the available tools based on Bioconductor and R packages differ in how they extract differential coexpression and at what level they study. There is a need for a user-friendly, flexible tool which can start analysis using raw or preprocessed microarray data and can report different levels of useful information. FINDINGS: We present a GUI software, No3CoGP: Non-Conserved and Conserved Coexpressed Gene Pairs which takes Affymetrix microarray data (.CEL files or log2 normalized.txt files) along with annotation file (.csv file), Chip Definition File (CDF file) and probe file as inputs, utilizes the concept of network density cut-off and Fisher's z-test to extract biologically relevant information. It can identify four possible types of gene pairs based on their coexpression relationships. These are (i) gene pair showing coexpression in one condition but not in the other, (ii) gene pair which is positively coexpressed in one condition but negatively coexpressed in the other condition, (iii) positively and (iv) negatively coexpressed in both the conditions. Further, it can generate modules of coexpressed genes. CONCLUSION: Easy-to-use GUI interface enables researchers without knowledge in R language to use No3CoGP. Utilization of one or more CPU cores, depending on the availability, speeds up the program. The output files stored in the respective directories under the user-defined project offer the researchers to unravel condition-specific functionalities of gene, gene sets or modules. More... »

PAGES

886

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1756-0500-7-886

DOI

http://dx.doi.org/10.1186/1756-0500-7-886

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1050523893

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25487059


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