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ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data
2016
Nucleic Acids Research
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ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. ...
We identified thousands of binding motif matrices and their binding sites from ChIP-seq data of DNAbinding proteins and predicted millions of transcriptional regulatory relationships between transcription ...
Our database provides with multiple selectors and parameters to analyze the transcriptional regulatory relationships of TF-gene for all web-based modules and tools. In Figure S2) . ...
doi:10.1093/nar/gkw965
pmid:27924033
pmcid:PMC5210649
fatcat:e32fbug2v5bvnmi7gyajy2pzkq
Gene co-expression analysis for functional classification and gene–disease predictions
2017
Briefings in Bioinformatics
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Acknowledgements We thank the members of the Integrative Genomics of Ageing Group for useful suggestions and discussions. ...
Finally, we thank the Institute of Integrative Biology at the University of Liverpool for supporting the PhD studies of Sipko van Dam. ...
ChIP-seq This method uses the same approach as ChIP-chip, but using RNA-seq rather than microarray to identify TFBSs. Clustering A statistical method of grouping variables. ...
doi:10.1093/bib/bbw139
pmid:28077403
pmcid:PMC6054162
fatcat:meqto5bjubd33egrudekf52y7e
Epigenetic modulation of brain gene networks for cocaine and alcohol abuse
2015
Frontiers in Neuroscience
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Clustering analysis of variation from whole-genome sequencing of gene expression (RNA-Seq) and histone H3 lysine 4 trimethylation (H3K4me3) events (ChIP-Seq) revealed the underlying structure of the transcriptional ...
Repeated exposure to cocaine and alcohol leads to longstanding changes in gene expression, and subsequent functional CNS plasticity, throughout multiple brain regions. ...
Supplemental Table 6 | WGCNA assignment of gene modules for RNA-Seq and ChIP-Seq experiments. ...
doi:10.3389/fnins.2015.00176
pmid:26041984
pmcid:PMC4438259
fatcat:5i2dcqv45bbxxer5g4d56srh6e
Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell
2012
Journal of Integrative Bioinformatics
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Genome wide ChIP-seq TF binding maps in mouse stem cells include Oct4, Sox2, Nanog, Tbx3, Smad2 as well as group of other factors. ...
ChIP-seq allows study of new candidate transcription factors for reprogramming. It was shown that Nr5a2 could replace Oct4 for reprogramming. ...
Acknowledgements The statistics of TF binding using publicly available ChIP-seq data was updated using highthroughput computer cluster "Bioinformatics" SB RAS. ...
doi:10.1515/jib-2012-211
fatcat:p5xkzdkfnne53o4bg4qny4boju
An integrated ChIP-seq analysis platform with customizable workflows
2011
BMC Bioinformatics
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The next step consists of interpreting the biological meaning of the peaks through their association with known genes, pathways, regulatory elements, and integration with other experiments. ...
The first step in ChIP-seq data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence reads). ...
Kemerlis, for their suggestions in the revision of this manuscript. ...
doi:10.1186/1471-2105-12-277
pmid:21736739
pmcid:PMC3145611
fatcat:b566plvi35hjhprw3evdqx2gjy
Applications of integrative OMICs approaches to gene regulation studies
2016
Quantitative Biology
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We highlight the advantages of these methods, particularly in elucidating molecular basis of biological regulatory mechanisms. ...
Functional genomics employs dozens of OMICs technologies to explore the functions of DNA, RNA and protein regulators in gene regulation processes. ...
This article does not contain any studies with human or animal subjects performed by any of the authors. ...
doi:10.1007/s40484-016-0085-y
fatcat:z5ei3ztspne2lmczdca4w4z4za
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
2020
Genome Biology
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Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. ...
Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. ...
To boost the performance of TF ChIP-seq or imputed TF binding data in the identification of regulatory TRs, we developed Lisa chromatin landscape models, which use H3K27ac ChIP-seq and DNase-seq chromatin ...
doi:10.1186/s13059-020-1934-6
pmid:32033573
fatcat:bi6xn7silzcfze57tsfdnypy6u
Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer
2020
Cancer Cell International
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Next, we pinpointed the transcription factors AR and HSF1 as the regulatory co-factors of KLF5 through bioinformatics analysis. ...
Then we analyzed the motif pattern of the binding regions for the lncRNA targets. The regulatory co-factors of KLF5 were then searched for through bioinformatics analysis. ...
Weiling He from the Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, who provided suggestions for this study. ...
doi:10.1186/s12935-020-01527-x
pmid:32943987
pmcid:PMC7487661
fatcat:yskwgwe53neuxl6xtjdge5nrbe
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis
2015
Scientific Data
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Further, we describe the use of TF overexpression datasets to validate a global gene regulatory network model of MTB and describe an online source to explore the datasets. ...
We also define elaborate quality control measures, extensive filtering steps, and the gene-level overlap between ChIP-seq and microarray datasets. ...
(b) Table of TFs that bind with close proximity of a given gene from ChIP-seq experiments is listed on the gene page. ...
doi:10.1038/sdata.2015.10
pmid:25977815
pmcid:PMC4413241
fatcat:nlh27ehml5bfxanexr7yet5xra
Systematic identification of conserved motif modules in the human genome
2010
BMC Genomics
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Compared with 14 ChIP-seq experiments, on average, our methods predicted 69.6% of ChIP-seq peaks with TFBSs of multiple TFs. ...
There are 30 motifs corresponding to 13 TFs used in these ChIP-seq experiments. ...
Additional material Additional file 1: The readme file of the ChIP-seq data analysis. This file describes the ChIP-seq data used and the analysis of ChIP-seq data performed. ...
doi:10.1186/1471-2164-11-567
pmid:20946653
pmcid:PMC3091716
fatcat:nmigm7s7fzhl7jsikhm3vldulm
An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury
2013
BMC Genomics
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Our approach combined mRNA and microRNA expression profiling data, ChIP-Seq data of transcription factors, and computational transcription factor and microRNA target prediction. ...
Conclusions: This work demonstrates a systematic method for gene regulatory network inference that may be used to gain new information on gene regulation by transcription factors and microRNAs. ...
Siteman Cancer Center and by ICTS/CTSA Grant UL1RR024992 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research ...
doi:10.1186/1471-2164-14-84
pmid:23387820
pmcid:PMC3599357
fatcat:nkwqdno56jebxgljmyzv737ony
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data
2017
Briefings in Bioinformatics
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The bottleneck, however, is the lack of robust mathematical models, as well as efficient computational methods for TFBS prediction to make effective use of massive ChIP-seq data sets in the public domain ...
Hence, prediction of transcription factor binding sites (TFBSs) provides a solid foundation for inferring gene regulatory mechanisms and building regulatory networks for a genome. ...
identify the motifs associated with cofactors of the ChIP-ed TF [73] or cis-regulatory modules [78] ; (iii) lack of insight in integration of ChIP-seq data sets from multiple TFs [79] ; (iv) the traditional ...
doi:10.1093/bib/bbx026
pmid:28334268
fatcat:m4kvr736ojfz3jtwgxh6euisua
Regulatory analysis of the C. elegans genome with spatiotemporal resolution
2014
Nature
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Large-scale survey of regulatory binding As part of the modENCODE consortium, we performed 241 ChIP-seq experiments to identify in vivo binding sites for 92 (10%) C. elegans transcription factors and regulatory ...
We determined the genomic distribution of binding sites for 92 transcription factors and regulatory proteins across multiple stages of Caenorhabditis elegans development by performing 241 ChIP-seq (chromatin ...
Recently, ref. 41 suggested regions with artefactual enrichment of ChIP-seq signals calling into question the validity of regions of high-occupancy where multiple ChIP-seq experiments produce enrichments ...
doi:10.1038/nature13497
pmid:25164749
pmcid:PMC4530805
fatcat:u4oac5x6ajfrzdcjgfzww3gfgu
Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells
2019
Frontiers in Genetics
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We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins clustered within different chromatin states. ...
These chromatin-state-specific regulatory modules were found to have significant influence on gene expression. ...
Recently, efforts have been devoted to integrate multiple ChIP-seq datasets to uncover protein-protein interactions. ...
doi:10.3389/fgene.2018.00731
pmid:30697231
pmcid:PMC6341026
fatcat:pbn6fmnenzhs7eulcxvtj57h74
Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays
2009
Molecular Biosystems
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Co-occurrences are reflected in overlapping and adjacent signals in multiple ChIP or DamID profiles. ...
We provide a simple guide to some of the statistical tools used by these methods. † This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology. ...
Sarah Bray (Department of Physiology, Development and Neuroscience, University of Cambridge). ...
doi:10.1039/b906880e
pmid:19763325
pmcid:PMC3475982
fatcat:zvbdab35nvc6th2ngscj7ihqfq
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