Analysis of Common Regulators

platelet-derived growth factor COL18A1 NRCAM COL7A1 SP1 catenin thrombin integrin RAC1 TIAM1 RAS small monomeric GTPase TNFRSF6 integrin Phosphatidylinositol 3-kinase EGR1 - MT1A catenin - CD44 TIAM1 - CD44 Nodes: integrin - RAC2 TGFB1 - SGK platelet-derived growth factor - CD44 TGFB1 - COL7A1 Nodes: IL1B - HNMT PKC - DSP TNFRSF6 - CD44 TGFB1 - DAF LPA - AKAP12 platelet-derived growth factor - AKAP12 INS - PFKFB3 MAPK1 - HNRPC Nodes: IL1B - DAF integrin - CD44 SRC - AKAP12 TGFB1 - COMP thrombin - SGK TGFB1 - CD44 LPA - GYPC RAC1 - CD44 SP1 - CD44 TNFRSF6 - RAC2 PKC - AKAP12 RAS small monomeric GTPase - RAC2 SP1 - ADH5 integrin - RAC2 MMP14 - MT1A SRC - COL18A1 MAPK1 - SGK AKT1 - ARK5 MAPK1 - NEDD4 AKT1 - SGK Node between RAC1 and RAC2 SRC - CD44 Phosphatidylinositol 3-kinase - CD44 Node between TIAM1 and RAC2 RAS small monomeric GTPase - CD44 Nodes: Phosphatidylinositol 3-kinase - RAC2 catenin - NRCAM SGK - NEDD4 INS - SGK PKC - CD44 MMP14 - CD44 EGR1 - CD44 integrin - CD44 thrombin - RAC2 PKC LPA ARK5 RAC2 HNRPC GYPC DSP ADH5 PFKFB3 MAPK1 SRC AKAP12 MMP14 HNMT DAF TGFB1 SGK NEDD4 CD44 COMP MT1A INS IL1B EGR1 AKT1

FIGURE 3B. Analysis for common regulators.  First 71 genes differentially expressed during class comparisons was used in this analysis (nominal p=0.006). PathwayAssist (Ariadne Genomics, Rockville, MD) a software tool for biological pathway analysis was used. It relies on ResNet, a database specifically targeted at the extracting data from the language of scientific abstracts from PubMed in order to identify relationships among genes, visualize pathways, gene regulation networks and protein interactions. This analysis used ResNet 3.0 (Medline August, 24,2004). To simplify the network, genes that could not be linked together were removed. Genes that are increased in SSc fibroblasts are colored red, and genes that are decreased colored pink. Genes that  inserted by Pathway Assist to link the genetic networks are colored gray. The boxes on the arrows are hyperlinks indicating relationships of the genes and targets.

Analysis of Common Regulators