Journal: BMC Genomics

Article Title: Liver transcriptome analysis of Atlantic cod ( Gadus morhua ) exposed to PCB 153 indicates effects on cell cycle regulation and lipid metabolism

doi: 10.1186/1471-2164-15-481

Figure Lengend Snippet: A statistically significant network of interactions within the differentially regulated genes. The “Direct interaction” algorithm in MetaCore was used for generation of the interaction networks. Only genes with direct connections in the network are shown.

Article Snippet: Analysis of the differentially regulated genes using the functional ontologies in MetaCore (GeneGo pathway map, process network and GO process) resulted in significant enrichment of many pathways and networks mainly related to lipid metabolism, cell cycle, tissue remodeling and wound repair, immune response, stress response, apoptosis and various signaling pathways (Table , Additional file : Tables S2-4).

Techniques:

Journal: PLoS ONE

Article Title: Molecular Markers of Tubulointerstitial Fibrosis and Tubular Cell Damage in Patients with Chronic Kidney Disease

doi: 10.1371/journal.pone.0136994

Figure Lengend Snippet: ( A ) Distribution of differences in gene expression between control kidney RNA (Control) and RNA extracted from 48 CKD biopsies. Microarray analysis was performed and genes down-regulated (z-score < -2.0, green) or up-regulated (z-score > 2.0, blue) in CKD are indicated. ( B ) Biological functions of the genes showing differential expression in CKD samples were classified according to their Gene Ontology and P values were calculated with MetaCore software. ( C ) Relationship between P values from Kruskal-Wallis test on tubulointerstitial fibrosis and tubular cell damage. Each symbol represents one gene. Gray or black circles indicate genes with any P values < 0.05; open circles represent genes with both P values > 0.05. HAVCR1, hepatitis A virus cellular receptor 1; LCN2, lipocalin 2; SOX9, SRY-box 9; WFDC2, WAP four-disulfide core domain 2; NKX6-2, NK6 homeobox 2.

Article Snippet: These genes were classified according to their function using MetaCore Software (GeneGo, St. Joseph, MI).

Techniques: Gene Expression, Control, Microarray, Quantitative Proteomics, Software, Virus

Journal: PLoS ONE

Article Title: Cartilage-Specific Ablation of Site-1 Protease in Mice Results in the Endoplasmic Reticulum Entrapment of Type IIB Procollagen and Down-Regulation of Cholesterol and Lipid Homeostasis

doi: 10.1371/journal.pone.0105674

Figure Lengend Snippet: ( A ) A schematic representation of the top ten biological pathways up-regulated in S1P cko chondrocytes identified by GeneGo (MetaCore) based on their p value. The majority of up-regulated pathways belong to UPR in response to ER stress. ( B ) A molecular network generated from upregulated genes with the addition of ATF6α to the network. Green lines represent activation and red lines represent inhibition.

Article Snippet: Differential gene expression data derived from microarray analysis was used to identify functional and molecular networks through the use of MetaCore GeneGo network building tools (GeneGo Inc., Carlsbad, CA).

Techniques: Generated, Activation Assay, Inhibition