Construction of gene/protein interaction networks for primary myelofibrosis and KEGG pathway-enrichment analysis of molecular compounds

Abstract

ABSTRACT. The objective of this study was the development of a gene/ protein interaction network for primary myelofibrosis based on gene expression, and the enrichment analysis of KEGG pathways underlying the molecular complexes in this network. To achieve this, genes involved in primary myelofibrosis were selected from the OMIM database. A gene/ protein interaction network for primary myelofibrosis was obtained through Cytoscape with the literature mining performed using the Agilent Literature Search plugin. The molecular complexes in the network were detected by ClusterViz plugin and KEGG pathway enrichment of molecular complexes was performed using DAVID online. We found 75 genes associated with primary myelofibrosis in the OMIM database. The gene/protein interaction network of primary myelofibrosis contained 608 nodes, 2086 edges, and 16127 Gene/protein interaction networks and enrichment analysis ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 16126-16132 (2015) 4 molecular complexes with a correlation integral value greater than 4. Molecular complexes involved in KEGG pathways are related to cytokine regulation, immune function regulation, ECM-receptor interaction, focal adhesion, actin cytoskeleton regulation, cell adhesion molecules, and other biological behavior of tumors, which can provide a reliable direction for the treatment of primary myelofibrosis and the bioinformatic foundation for further understanding the molecular mechanisms of this disease.

Transcriptomic Profile Analysis of Populus talassica × Populus euphratica Response and Tolerance under Salt Stress Conditions

“…The KEGG database is comprehensive, integrating genomic, chemical, and system functional information. Both GO and KEGG enrichment analyses used padj <0.05 as the threshold for significant enrichment [ 54 ]. In BP, enrichment was most concentrated in cellular processes and metabolic processes.…”