This movie shows a demo of importing and analyzing ChIP-Seq data in BED files (GSE11431) for analyzing promoter regions of genes. This is also useful if you have ChIP-on-chip data sets on promoter arrays.
Analyzing ChIP-seq data (GSE11431)
Data Source:
Download the SOA file.
You can download the SOA file of GSE11431. (1.17GB) Select "Import Archive..." under the Platform menu to import an SOA file into Subio Platform.
* This is a bit old. "Biological Table" is now called as "Genome," and tools of Annotation Analysis Plug-in and Genomic Analysis Plug-in are now merged into Advanced Plug-in.
Data Source
Summary
Transcription factors and their specific interactions with targets are crucial in specifying gene expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem cells, we use chromatin immunoprecipitation coupled to ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of thirteen sequence specific transcription factors (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1 and CTCF) and two transcription regulators (p300 and Suz12). These factors are known to play different roles in ES cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators and key reprogramming factors. Our study provides insights into the integration of the signaling pathways to the ES cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different transcription factors. Collectively, the comprehensive mapping of transcription factor binding sites identifies important features of the transcriptional regulatory networks that define ES cell identity.
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
https://www.cell.com/retrieve/pii/S009286740800617X