They write "gene expression changes mapped to 219 molecular interaction pathways and 1620 gene ontology groups".
Even the position of proteins in molecular interaction pathways (upstream or downstream) accounts for some variance in evolutionary rate [ 4].
The rice gene ontology (GO) categories were downloaded from the GO database (, 2008) and metabolic and molecular interaction pathways were identified in the KEGG database.
Here, we presented a novel framework that assigns biological context to molecular interaction pathways while allowing for context variations and switches that may not be obvious to the outside observer before our analysis.
Previous context-sensitive approaches to network interpretation limited molecular interaction pathways to a single context, such as a single tissue or cell type (Schaefer, 2012), or followed a predefined context-transition template, e.g. defining a flow from membrane to nucleus (Scott et al., 2006).
We further used IPA software to analyze 88 PFS-related genes from the viewpoint of molecular interaction or pathway.
InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.
For molecular interaction and pathway analyses of selected miRNAs, previously validated target genes from degradome sequencing [ 28, 40, 60] and microarray data [ 61] were recorded and their molecular interactions were illustrated by Cytoscape 2.8.2 [ 80].
PathwayAssist is supplied with ResNet molecular interaction and pathway database, which contains more than 500 000 functional links for more than 50 000 proteins, extracted from more than 5 000 000 Medline abstracts and full-length articles (ResNet update Q4 2004).
For a set of proteins or genes with enriched pathways and GOBPs, we propose a method that integrates molecular interaction, biological pathways and GOBP to standardize descriptions of pathways using GOBPs through the establishment of the functional biological pathway-process network.
