Journal: Nutrition & Metabolism

Article Title: Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)

doi: 10.1186/1743-7075-7-56

Figure Lengend Snippet: The highest G-score networks and corresponding processes identified using MetaCore [ 50 ]

Article Snippet: Array data analysis was performed using R http://www.R-project.org and GeneGo MetaCore (GeneGo bioinformatics software, Inc.).

Techniques: Binding Assay

Journal: Cancer research

Article Title: Dramatic antitumor effects of the dual MET/RON small-molecule inhibitor LY2801653 in non-small cell lung cancer

doi: 10.1158/0008-5472.CAN-12-3583

Figure Lengend Snippet: A. The protein tyrosine kinase activity profile obtained by using H1993 lysates treated with LY2801653 (3 nM) as tested on PamChip® microarrays. The color-coded response signature is shown as a heatmap where treatment-related upregulation of kinase activity is reflected by red and a decrease by blue. The protein tyrosine kinase activity is down regulated in a concentration-dependent manner for most peptides. B. Thirteen significant tyrosine kinase substrate modulation by LY2801653 (3 nM) treatment as tested on PamChip® microarrays is shown (*: p-value <0.05, paired-two-tailed Student’s t test). C. Network between the PamGene significant genes associated with H1993 treatment with LY2801653 (3 nM) using MetaCore™ (GeneGo). Objects highlighted with green and blue represents ‘Initial and Intermediate object’ which means object chosen to build the pathways from and situated along the pathway. Object highlighted with blue and red represents ‘Intermediate and Terminal object’ which means object situated along the pathway and chosen to build the termination of pathways.

Article Snippet: Peptides found to be significantly down- or up-regulated in the statistical analysis (p<0.05) in PamGene were used for pathway and network analyses using the bioinformatics analysis software MetaCore TM (GeneGo, Thomson Reuters, St. Joseph, MI, USA) as described ( 22 , 23 ).

Techniques: Activity Assay, Concentration Assay, Two Tailed Test

Journal: Cancer research

Article Title: Dramatic antitumor effects of the dual MET/RON small-molecule inhibitor LY2801653 in non-small cell lung cancer

doi: 10.1158/0008-5472.CAN-12-3583

Figure Lengend Snippet: The Key Transcription Factors of H1993 treatment with LY2801653 (3 nM) Metacore ™ (GeneGo) analysis based on identified PamGene 12 siginificant genes ( ) which are modulated by LY2801653 treatment (3 nM). Note: ‘Total Nodes’ indicate the total number of genes analyzed whereas ‘Seed Nodes’ indicate the number of genes out of the Total Nodes that were involved with that particular transcription factor.

Article Snippet: Peptides found to be significantly down- or up-regulated in the statistical analysis (p<0.05) in PamGene were used for pathway and network analyses using the bioinformatics analysis software MetaCore TM (GeneGo, Thomson Reuters, St. Joseph, MI, USA) as described ( 22 , 23 ).

Techniques: Cell Surface Receptor Assay, Phospho-proteomics, Transduction