Computational protocol: MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation

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Protocol publication

[…] ChIP-seq datasets were obtained from the Encyclopedia of DNA Elements (ENCODE) Consortium (MYC ChIP-seq in HeLa-S3: ENCODE Data Coordination Centre (DCC) accession: ENCSR000EZD; SMARCB1/INI1 ChIPs-seq in HeLa-S3: DCC accession: ENCSR000EDK). Overlapping peaks of at least one nucleotide between 2 datasets were obtained using the intersection function of BEDTools version 2.18. Statistical analysis for coincident binding was determined using the GSC test; statistical significance was determined at p < 0.5. Putative target genes and genomic regions were identified using BETA version 1.0.6. GO analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) version 6.7. […]

Pipeline specifications

Software tools BEDTools, DAVID
Application ChIP-seq analysis
Organisms Homo sapiens
Diseases Neoplasms, Rhabdoid Tumor