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ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
2016 Nucleic Acids Research  
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

Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
2017 Briefings in Bioinformatics  
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

Sean P. Farris, Robert A. Harris, Igor Ponomarev
2015 Frontiers in Neuroscience  
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

Yuriy Orlov, Han Xu, Dmitri Afonnikov, Bing Lim, Jian-Chien Heng, Ping Yuan, Ming Chen, Junli Yan, Neil Clarke, Nina Orlova, Mikael Huss, Konstantin Gunbin (+2 others)
2012 Journal of Integrative Bioinformatics  
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

Eugenia G Giannopoulou, Olivier Elemento
2011 BMC Bioinformatics  
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

Jing Qin, Bin Yan, Yaohua Hu, Panwen Wang, Junwen Wang
2016 Quantitative Biology  
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

Qian Qin, Jingyu Fan, Rongbin Zheng, Changxin Wan, Shenglin Mei, Qiu Wu, Hanfei Sun, Myles Brown, Jing Zhang, Clifford A. Meyer, X. Shirley Liu
2020 Genome Biology  
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

Qi Liao, Linbo Chen, Ning Zhang, Yang Xi, Shiyun Hu, Derry Minyao Ng, Fatma Yislam Hadi Ahmed, Guofang Zhao, Xiaoxiang Fan, Yangyang Xie, Xiaoyu Dai, Yanping Jin (+4 others)
2020 Cancer Cell International  
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

Serdar Turkarslan, Eliza J R Peterson, Tige R Rustad, Kyle J Minch, David J Reiss, Robert Morrison, Shuyi Ma, Nathan D Price, David R Sherman, Nitin S Baliga
2015 Scientific Data  
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

Xiaohui Cai, Lin Hou, Naifang Su, Haiyan Hu, Minghua Deng, Xiaoman Li
2010 BMC Genomics  
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

Li-Wei Chang, Andreu Viader, Nobish Varghese, Jacqueline E Payton, Jeffrey Milbrandt, Rakesh Nagarajan
2013 BMC Genomics  
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

Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
2017 Briefings in Bioinformatics  
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

Carlos L. Araya, Trupti Kawli, Anshul Kundaje, Lixia Jiang, Beijing Wu, Dionne Vafeados, Robert Terrell, Peter Weissdepp, Louis Gevirtzman, Daniel Mace, Wei Niu, Alan P. Boyle (+6 others)
2014 Nature  
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

Sharmi Banerjee, Hongxiao Zhu, Man Tang, Wu-chun Feng, Xiaowei Wu, Hehuang Xie
2019 Frontiers in Genetics  
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

Audrey Qiuyan Fu, Boris Adryan
2009 Molecular Biosystems  
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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