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Series GSE72531 Query DataSets for GSE72531
Status Public on May 13, 2016
Title Reconstructing gene regulatory networks of tumorigenesis [SNP]
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 TFs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. These TFs are involved in the regulation of divers processes, including cell differentiation, immune response and establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes, which are not only co-regulated but also functionally related. Further decortication of TF targets enabled us to define potential key regulators of cell transformation, which are engaged in RNA metabolism and chromatin remodelling. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of gene regulatory networks that are altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.
Overall design Affymetrix SNP arrays (250K) were performed according to the manufacturer's directions on DNA extracted from BJ, BJEL and BJELM cells
Contributor(s) Malysheva V, Mendoza-Parra MA, Ashick M, Saleem M, Gronemeyer H
Citation(s) 27198694
Submission date Aug 31, 2015
Last update date May 17, 2017
Contact name Valeriya Malysheva
Organization name IGBMC
Street address 1 rue Laurent Fries
City Illkirch; Strasbourg
ZIP/Postal code 67404
Country France
Platforms (1)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (3)
GSM1868966 BJ_SNP_Affy_250K
GSM1868967 BJEL_SNP_Affy_250K
GSM1868968 BJELM_SNP_Affy_250K
This SubSeries is part of SuperSeries:
GSE72533 Reconstructing gene regulatory networks of tumorigenesis
BioProject PRJNA294768

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72531_Mapping250K_NSP.BJ_vs_BJEL.LOH.txt.gz 642.1 Kb (ftp)(http) TXT
GSE72531_Mapping250K_NSP.BJ_vs_BJEL.copy_number.txt.gz 5.4 Mb (ftp)(http) TXT
GSE72531_Mapping250K_NSP.BJ_vs_BJELM.LOH.txt.gz 637.2 Kb (ftp)(http) TXT
GSE72531_Mapping250K_NSP.BJ_vs_BJELM.copy_number.txt.gz 5.4 Mb (ftp)(http) TXT
GSE72531_RAW.tar 75.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record

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