Journal: The Journal of Biological Chemistry

Article Title: The role of Twist1 in mutant huntingtin–induced transcriptional alterations and neurotoxicity

doi: 10.1074/jbc.RA117.001211

Figure Lengend Snippet: Transcriptional regulatory network of mutant Htt–expressing cortical neurons. A mutant Htt–associated transcriptional network was generated from differentially expressed genes (FDR < 0.05, average CPM > 0.5) identified by RNA-Seq analysis with the primary cortical neuron model of HD, using GeneGo MetaCore as described under “Experimental procedures.” 77 interactions with 13 transcription factors (oval, |log2FC| > 1.5) and 20 targets (box, |log2FC| > 1) are shown. The connections between genes represent transcriptional regulation, protein binding, or posttranslational modification (phosphorylation). Color denotes log2FC. See also Table S5.

Article Snippet: The core regulatory network was assembled using the knowledge-based GeneGO MetaCore database from 1217 differentially expressed genes between Htt-72Q– and Htt-25Q–expressing cortical neurons in RNA-Seq analysis (genes with FDR < 0.05, |log 2 FC| > 1, and average CPM > 0.5 from Table S1 ) and was composed of 13 transcription factors (TFs) (|log 2 FC| > 1.5) that interact with one or more TFs and 20 target genes that are regulated by at least two of the 13 TFs, with a total of 77 interactions ( and Table S5 ).

Techniques: Mutagenesis, Expressing, Generated, RNA Sequencing Assay, Protein Binding, Modification

Journal: EBioMedicine

Article Title: Multi-Omics Analysis Reveals a HIF Network and Hub Gene EPAS1 Associated with Lung Adenocarcinoma

doi: 10.1016/j.ebiom.2018.05.024

Figure Lengend Snippet: Distribution of networks built by randomly selected genes. From a total of 24,847 genes, we randomly generated 6 sets of gene lists, with each set containing 100 gene lists. Each set contained 50, 100, 200, 300, 400, or 500 genes, denoted by R50, R100, R200, R300, R400, and R500, respectively. Networks were built from each gene list using MetaCore GeneGo database and were used to calculate a 95% CI curve. GWAS denotes network from GWAS data; FFPE denotes network from transcriptomic profiling data; and GWAS+FFPE+core denotes networks built from combining GWAS data, transcriptomic profiling data, and a core gene list.

Article Snippet: Networks were built from each gene list using MetaCore GeneGo database and were used to calculate a 95% CI curve.

Techniques: Generated