Integrative analysis of ChIP-chip and ChIP-seq dataset
LJ Zhu - Tiling arrays: Methods and protocols, 2013 - Springer
Epigenetic regulation and interactions between transcription factors and regulatory genomic
regions play crucial roles in controlling transcriptional regulatory networks that drive …
regions play crucial roles in controlling transcriptional regulatory networks that drive …
GTRD: a database on gene transcription regulation—2019 update
I Yevshin, R Sharipov, S Kolmykov… - Nucleic acids …, 2019 - academic.oup.com
The current version of the Gene Transcription Regulation Database (GTRD; http://gtrd.
biouml. org) contains information about:(i) transcription factor binding sites (TFBSs) and …
biouml. org) contains information about:(i) transcription factor binding sites (TFBSs) and …
[HTML][HTML] From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
[HTML][HTML] Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Abstract We developed Lisa (http://lisa. cistrome. org/) to predict the transcriptional
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …
[HTML][HTML] Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
MP Meers, D Tenenbaum, S Henikoff - Epigenetics & chromatin, 2019 - Springer
Background CUT&RUN is an efficient epigenome profiling method that identifies sites of
DNA binding protein enrichment genome-wide with high signal to noise and low sequencing …
DNA binding protein enrichment genome-wide with high signal to noise and low sequencing …
[HTML][HTML] Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
R Worsley Hunt, WW Wasserman - Genome biology, 2014 - Springer
Background The global effort to annotate the non-coding portion of the human genome
relies heavily on chromatin immunoprecipitation data generated with high-throughput DNA …
relies heavily on chromatin immunoprecipitation data generated with high-throughput DNA …
[HTML][HTML] Evaluation of algorithm performance in ChIP-seq peak detection
EG Wilbanks, MT Facciotti - PloS one, 2010 - journals.plos.org
Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq)
is revolutionizing our ability to interrogate whole genome protein-DNA interactions …
is revolutionizing our ability to interrogate whole genome protein-DNA interactions …
[HTML][HTML] ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Abstract ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions
enriched in a variety of ChIP-seq and related next-generation sequencing experiments …
enriched in a variety of ChIP-seq and related next-generation sequencing experiments …
ChIP-Enrich: gene set enrichment testing for ChIP-seq data
Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data.
Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene …
Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene …
[HTML][HTML] ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Background Transcription factor binding, histone modification, and chromatin accessibility
studies are important approaches to understanding the biology of gene regulation. ChIP-seq …
studies are important approaches to understanding the biology of gene regulation. ChIP-seq …