Computational protocol: Chemotherapy and terminal skeletal muscle differentiation in WT1‐mutant Wilms tumors

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Protocol publication

[…] RNA was isolated from the SIOP tumor samples as described in Ref. and from the other tumor samples with the RNeasy Mini Kit (Qiagen). The Wilms tumor samples used for RNA isolation are summarized in Table . Labeling of the RNA, microarray‐hybridization, and processing of the gene expression data was performed essentially as published previously . Heat maps were created with “pheatmap” available from CRAN (cran.r‐project.org). Gene expression data can be found at GEO: GSE63616 and GSE102723. To identify biological processes associated with gene expression profiles, the MetaCore software suite (http://thomsonreuters.com/metacore/) was used. The normalized microarray data from up‐ and down‐regulated data sets were uploaded into MetaCore. We selected genes with a minimum fluorescence intensity of 200 in at least one sample. The fold change (fc) and P‐values used for data analysis are shown in the individual sections. To study the difference between treated and untreated tumors, we first calculated the mean gene expression levels from the 11 chemotherapy‐treated and the seven untreated Wilms tumor samples. These gene sets were uploaded in MetaCore and analyzed using enrichment analysis of “process networks,” reflecting the content of a MetaCore database that was manually created based on GO processes, pathway maps, and network models of main cellular processes. […]

Pipeline specifications

Software tools PHeatmaps, MetaCore
Application Transcriptome data visualization
Organisms Homo sapiens
Diseases Neoplasms, Wilms Tumor