Computational protocol: Retinoblastoma protein promotes oxidative phosphorylation through upregulation of glycolytic genes in oncogene-induced senescent cells

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Protocol publication

[…] Total cellular RNA from two independent experiments was reverse-transcribed and hybridized to the Affymetrix U133 Plus 2.0 microarray, as described previously (Hino et al., ). Gene set enrichment analysis was performed using GSEA ver. 2.0 software provided by the Broad Institute of MIT and Harvard (http://www.broadinstitute.org/gsea/) (Subramanian et al., ). K-means clustering with the Euclidean distance was performed using MeV 4.8.1 (Saeed et al., ), and GO term analysis was carried out with the DAVID functional annotation tool (Dennis et al., ). RB enrichment in association with Cluster 20 genes (±2 kb from the transcription start site) was determined using PAVIS (Huang et al., ), based on previously reported RB ChIP-seq data in OIS IMR90 cells (Chicas et al., ). […]

Pipeline specifications

Software tools GSEA, DAVID, PAVIS
Application ChIP-seq analysis
Diseases Retinoblastoma