TFregulomeR reveals transcription factors' context-specific features and functions.
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Cites methods from "TFregulomeR reveals transcription f..."
...TF direct binding motifs surrounding p16 transcription start site were searched out using the TFregulomeR package, which is a TF motif analysis tool linking to 1,468 public TF ChIP-seq datasets in human (24)....
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...CTCF binding was analyzed in our study using ChIP-Seq data from cell lines analyzed by TFregulomeR (FB8470, GM12891, GM19240, prostate epithelial cells, and H1-derived mesenchymal stem cells)....
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...Bioinformatic analysis TF bindings and motif Analysis TF direct binding motifs surrounding p16 transcription start site were searched out using the TFregulomeR package, which is a TF motif analysis tool linking to 1,468 public TF ChIP-seq datasets in human (24)....
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...WGBS methylation data were collected from SNU-398 cells (both wild type and Decitabine treated) performed in our study; histone mark enrichments determined by ChIP-seq cross 7 cell lines (GM12878, H1-hESC, HSMM, HUVEC, K562, NHEK, NHLF) obtained from ENCODE; CTCF binding was analyzed in our study using ChIP-Seq data from cell lines analyzed by TFregulomeR (FB8470, GM12891, GM19240, prostate epithelial cells, and H1-derived mesenchymal stem cells)....
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...Using the motif analysis tool TFregulomeR (24), a TF binding site analysis tool linking to a large compendium of ChIP-seq data, we found CTCF (CCCTC-binding factor) binding peaks in exon 1 across five different cell lines (Fig....
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References
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"TFregulomeR reveals transcription f..." refers methods in this paper
...Briefly, relying on the Irreproducibility Discovery Rate (IDR) (24), ChIP-seq peaks were standardly called using MACS2 (25), followed by a motif de novo enrichment analysis with MEME-ChIP (11), focusing on regions defined by a ±100 bp window around peak summits....
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"TFregulomeR reveals transcription f..." refers methods in this paper
...At last, objects generated by the TFregulomeR package are compatible with thirdparty packages such as TFBSTools, which provides means for TFBS matrix handling and motif scanning (30), and rGREAT, for ontology analysis (32)....
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...Functional annotation was achieved using rGREAT, a GREAT analysis API (32)....
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...TFregulomeR compendium is accessible via an effective R-package application program interface (API), called TFregulomeR....
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...This API offers the required functions for easy data access, analysis and integration in pipelines....
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