ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2009
Exhaustive search for over-represented DNA sequence motifs with CisFinder.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data.NAR genomics and bioinformatics · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- Targeting Lin28 axis enhances glypican-3-CAR T cell efficacy against hepatic tumor initiating cell population.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- Freezing firefly algorithm for efficient planted (ℓ, d) motif search.Medical & biological engineering & computing · 2022Article
- A survey on deep learning in DNA/RNA motif mining.Briefings in bioinformatics · 2021Article
- Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells.Genes & development · 2021Article
- Bayesian Markov models improve the prediction of binding motifs beyond first order.NAR genomics and bioinformatics · 2021Article
- Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord.Frontiers in cell and developmental biology · 2021Article
- Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse.Nucleic acids research · 2020Article
- A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.Entropy (Basel, Switzerland) · 2019Article
- Article
- RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.Nucleic acids research · 2018Article
- Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming.Cellular and molecular life sciences : CMLS · 2018Review
- TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.BMC genomics · 2018Article
- Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision throughThe Biochemical journal · 2018Article
- Performance evaluation for MOTIFSIM.Biological procedures online · 2018Article
- The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation.Scientific reports · 2017Article
- GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences.
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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 Socratic graph.