ReviewBiology direct2014
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.
Review in Biology direct, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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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
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Improved linking of motifs to their TFs using domain information.Bioinformatics (Oxford, England) · 2020Pooled it
- HBMC bioinformatics · 2025Article
- The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.BMC bioinformatics · 2024Article
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Guidelines on the performance evaluation of motif recognition methods in bioinformatics.Frontiers in genetics · 2023Article
- A systematic study of HIF1A cofactors in hypoxic cancer cells.Scientific reports · 2022Article
- Article
- Finding de novo methylated DNA motifs.Bioinformatics (Oxford, England) · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- MODSIDE: a motif discovery pipeline and similarity detector.BMC genomics · 2018Article
- Performance evaluation for MOTIFSIM.Biological procedures online · 2018Article
- Association between genetic variants in p53 binding sites and risks of osteosarcoma in a Chinese population: a two-stage case-control study.Cancer biology & therapy · 2018Article
- Perinatal lead (Pb) exposure results in sex and tissue-dependent adult DNA methylation alterations in murine IAP transposons.Environmental and molecular mutagenesis · 2017Article
- MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia.Genome biology and evolution · 2017Article
- Maps of context-dependent putative regulatory regions and genomic signal interactions.Nucleic acids research · 2016Article
- Evaluating tools for transcription factor binding site prediction.BMC bioinformatics · 2016Article
- Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research.Progress in retinal and eye research · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.
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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.