ChIP-Seq
ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa.
... a ChIP-Seq was performed and identified regions of the genome that are bound by ...of ChIP-Seq and RNA-Seq to define the comprehensive regulon of a bifunctional transcriptional ...
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ChIP-seq analysis of histone H3K9 trimethylation in peripheral blood mononuclear cells of membranous nephropathy patients
... approaches, ChIP-seq enables the genome wide identification of binding sites of transcription factors and other DNA-binding proteins ...of ChIP-grade antibodies, ChIP-seq has become one ...
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An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.
... event ChIP enrichment, we ran the complete MultiGPS model on 14 ChIP-seq experiment sets in which the ENCODE2 project has performed replicated ChIP-seq of a given protein in all three ...
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Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
... by ChIP-seq using specific antibodies in HeLa ...of ChIP-seq and RNA-seq data revealed that UPS22 bound to the promoters of 56 ...
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Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina.
... independent ChIP-seq assays, we identified consistent sets of Otx2-bound cis-regulatory ...Otx2 ChIP-seq data shows that Otx2 occupies different functional domains of the genome in RPE cells ...
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CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis.
... using ChIP-Seq has emerged as an alternative to ChIP-chip ...methods. ChIP- Seq technology offers many advantages over ChIP-chip arrays, including but not limited ...
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PAPST, a User Friendly and Powerful Java Platform for ChIP-Seq Peak Co-Localization Analysis and Beyond.
... Assignment of super enhancers to key ESC genes by proximity. PAPST can quickly as- sign a set of genomic regions such as ChIP-Seq peaks to genes by proximity to their transcrip- tion start site (TSS). Using ...
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Evaluation of algorithm performance in ChIP-seq peak detection.
... Specificity. Assessing the rate of false positives in the peak lists is a challenging task. The available set of qPCR-determined negative sites for NRSF provides only 30 ‘‘true negatives’’, defined as sites where ...
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Enhanced regulatory sequence prediction using gapped k-mer features.
... of ChIP-seq peaks produced by the ENCODE uniform processing pipeline containing at least 500 regions (see ...in ChIP- seq data sets for CTCF and members of the cohesin complex (RAD21, SMC3) ...
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ePIANNO: ePIgenomics ANNOtation tool.
... many ChIP-seq web servers and databases have been developed to provide solu- tions for diverse biological ...a ChIP-seq database for chro- matin regulators and histone modification linkages in ...
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Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.
... TF ChIP-seq peaks among newly predicted CRMs, excluding training ...correct ChIP-seq peaks, compared to only 17 of the 45 Mk models (Fig ...correct ChIP-seq ...
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iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
... on ChIP peaks only (see Materials and ...the ChIP peak data (p-value = ...high ChIP peak, namely PLK3 and DDB2, were missed by ...small ChIP peak but have not been predicted by iRegulon as ...
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Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions.
... 60 ChIP-seq datasets), thus we may have specifically missed cofactors that are associated with other cardinal ...that ChIP- seq data for those cofactors that are specifically associated with ...
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Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers.
... We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 ...
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Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.
... Our ChIP-Seq analyses demonstrate that SWI/SNF components overlap extensively with important regions that require tight control of the dynamics of nucleosome occupancy such as promoters, enhancers and CTCF ...
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Sorafenib inhibits epithelial-mesenchymal transition through an epigenetic-based mechanism in human lung epithelial cells.
... Recently, the successful development of small chemicals that disrupt several fundamental signaling pathways has signified a paradigm shift in medical therapies [9]. In addition to this established molecular-targeting ...
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Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.
... This table describes the data used for this study. The main data includes five cell lines from both University of Washington (UW) and Duke University (Duke). Bias from this data has been illustrated in Figure 1 panels ...
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Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.
... CLAMP ChIP-seq signal enrichments at GA-repeats of different lengths are given for the X- chromosome (red) and autosomes (blue) from male S2 (top) and female Kc cells ...
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Genome-wide discovery of drug-dependent human liver regulatory elements.
... Previous reports have found enhancers to be responders of drug treatment [24–27]. Our functional validation results broadly suggest that promoters on their own are largely incapable of driving the effects of rifampin ...
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Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer.
... detailed ChIP-seq and RNA-seq analysis of HIF-α isoform binding site occupancy and gene expression in the pVHL-defective CCRC 786–0 cell line, fol- lowing re-expression of HIF-1α or overexpression of ...
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