ArticleBioinformatics (Oxford, England)2011
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed.
- BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells.Breast cancer research : BCR · 2019Article
- ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes.PloS one · 2018Article
- Genomic feature extraction and comparison based on global alignment of ChIP-sequencing data.Bioengineered · 2017Article
- Features that define the best ChIP-seq peak calling algorithms.Briefings in bioinformatics · 2017Article
- Article
- iHMS: a database integrating human histone modification data across developmental stages and tissues.BMC bioinformatics · 2017Article
- COPAR: A ChIP-Seq Optimal Peak Analyzer.BioMed research international · 2017Article
- The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.BMC genomics · 2016Article
- EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition.Cancer research · 2016Article
- Methyl-binding DNA capture Sequencing for Patient Tissues.Journal of visualized experiments : JoVE · 2016Article
- Identifying peaks in *-seq data using shape information.BMC bioinformatics · 2016Article
- Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.BioMed research international · 2016Article
- Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer.Nature communications · 2015Article
- Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer.The EMBO journal · 2015Article
- Transcriptional regulation and spatial interactions of head-to-head genes.BMC genomics · 2014Article
- A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.Biology direct · 2014Review
- AnnotateGenomicRegions: a web application.BMC bioinformatics · 2014Article
- Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data.BMC bioinformatics · 2013Article
- ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes.Epigenetics & chromatin · 2013Article
- Estimation of CpG coverage in whole methylome next-generation sequencing studies.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
unlabelledChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, few of them are available as easy-accessible online web tools for processing both ChIP-chip and ChIP-seq data for the ChIP-based user community. As such, we have developed a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks with GFF, BED, bedGraph and .wig formats, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results via a user-friendly web interface. AVAILABILITY: http://motif.bmi.ohio-state.edu/W-ChIPeaks/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.