GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways

Cluster analysis of rat pancreatic islet gene mRNA levels after culture in low-, intermediate- and high-glucose concentrations

“…Although gene ontology categories were sometimes enriched in neighbouring clusters, we were able to identify biological processes that are mostly downor upregulated between low and intermediate, intermediate and high, or low and high glucose, as well as processes regulated in a complex manner. To better convey our main findings, we drew biological maps combining selected pathways of interest using MAPP-Builder [37], and coloured genes according to the cluster to which they belong using GenMAPP 2.1 (http://www.genmapp.org, accessed 1 December 2008) [37] (Figs. 4, 5, ESM Fig.…”

“…4 Glucose-induced changes in the mRNA levels of genes involved in islet cell nutrient metabolism, hormone production and ion handling. New biological maps were created by combining selected biological maps of interest available on GenMAPP database with data from the literature and various public databases using MAPP Builder software [37]. Genes involved in selected metabolic and signalling pathways were then coloured according to the cluster or pair of clusters to which they belong using GenMAPP 2.1 (cluster pairs as in Fig.…”

Renal macrophage migration and crystal phagocytosis via inflammatory-related gene expression during kidney stone formation and elimination in mice: Detection by association analysis of stone-related gene expression and microstructural observation

“…Data files were analyzed using pathway information of the Gene Map Annotator and Pathway Profiler (GenMAPP), (16) one of the attached functions of GeneSpring 7.3 consisting of hundreds of premade pathway maps for pathway identification, and the categories of cytokines and inflammatory response (BioCarta) and the inflammatory response pathway were sorted based on our previous data. (15) Association analysis of the detected gene expression value with crystal amount and macrophage-related gene Based on the expression values of selected genes by microarray analysis, (15) linear regression analysis was used to determine the relationship between each gene expression value and the quantified renal crystal amount and expression value of epidermal growth factor (EGF)-like module containing the mucin-like hormone receptor-like sequence 1 (Emr1) encoding F4/80, a mouse monocyte/macrophage-specific surface marker.…”

A bioinformatical and functional approach to identify novel strategies for chemoprevention of colorectal cancer

“…In our analysis, we assembled gene sets from well accepted and widely used curated pathway databases. A total of 169 functional gene sets as reported in the KEGG, 109 from the GenMAPP, and 187 as reported in the Biocarta database (http://www.biocarta.com/) were analyzed (Dahlquist et al, 2002;Kanehisa et al, 2006).…”