Results 1 - 10
of
72
JASPAR, the open access database of transcription factorbinding profiles: new content and tools in the 2008 update
- Nucleic Acids Res
, 2008
"... factor-binding profiles: new content and tools in the 2008 update ..."
Abstract
-
Cited by 96 (0 self)
- Add to MetaCart
(Show Context)
factor-binding profiles: new content and tools in the 2008 update
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
- Nucleic Acids Res
, 2009
"... and GABP identified at regulatory DNA elements through ChIP-sequencing ..."
Abstract
-
Cited by 12 (0 self)
- Add to MetaCart
(Show Context)
and GABP identified at regulatory DNA elements through ChIP-sequencing
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. 2012; 487: p
"... transformation ..."
Localized motif discovery in gene regulatory sequences
, 2010
"... Motivation: Discovery of nucleotide motifs that are localized with respect to a certain biological landmark is important in several appli-cations, such as in regulatory sequences flanking the transcription start site, in the neighborhood of known transcription factor binding sites, and in transcript ..."
Abstract
-
Cited by 10 (0 self)
- Add to MetaCart
Motivation: Discovery of nucleotide motifs that are localized with respect to a certain biological landmark is important in several appli-cations, such as in regulatory sequences flanking the transcription start site, in the neighborhood of known transcription factor binding sites, and in transcription factor binding regions discovered by massively parallel sequencing (ChIP-Seq). Results: We report an algorithm called LocalMotif to discover such localized motifs. The algorithm is based on a novel scoring function, called spatial confinement score, which can determine the exact interval of localization of a motif. This score is combined with other existing scoring measures including over-representation and relative entropy to determine the overall prominence of the motif. The approach successfully discovers biologically relevant motifs and their intervals of localization in scenarios where the motifs cannot be discovered by general motif finding tools. It is especially useful for discovering multiple co-localized motifs in a set of regulatory sequences, such as those identified by ChIP-Seq. Availability and Implementation: The LocalMotif software is available at
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins
- Nucleic Acids Res
, 2014
"... Proteins with sequence-specific DNA binding function are important for a wide range of biological activities. De novo prediction of their DNA-binding specificities from sequence alone would be a great aid in inferring cellular networks. Here we introduce a method for predicting DNA-binding specifici ..."
Abstract
-
Cited by 9 (2 self)
- Add to MetaCart
Proteins with sequence-specific DNA binding function are important for a wide range of biological activities. De novo prediction of their DNA-binding specificities from sequence alone would be a great aid in inferring cellular networks. Here we introduce a method for predicting DNA-binding specificities for Cys2His2 zinc fingers (C2H2-ZFs), the largest family of DNA-binding proteins in metazoans. We develop a general approach, based on empirical calculations of pairwise amino acid–nucleotide interaction energies, for predicting position weight matrices (PWMs) representing DNA-binding specificities for C2H2-ZF proteins. We predict DNA-binding specificities on a per-finger basis and merge predictions for C2H2-ZF domains that are arrayed within sequences. We test our approach on a diverse set of natural C2H2-ZF proteins with known binding specificities and demonstrate that for>85 % of the proteins, their predicted PWMs are accurate in 50 % of their nucleotide positions. For proteins with several zinc finger isoforms, we show via case studies that this level of accuracy enables us to match isoforms with their known DNA-binding specificities. A web server for predict-ing a PWM given a protein containing C2H2-ZF domains is available online at
Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1
- Nucleic Acids Res
, 2010
"... We used mouse hepatic chromatin enriched with an FXR antibody and chromatin immunoprecipitation-sequencing (ChIP-seq) to evaluate FXR binding on a genome-wide scale. This identified 1656 FXR-binding sites and 10 % were located within 2 kb of a transcription start site which is much higher than predi ..."
Abstract
-
Cited by 7 (0 self)
- Add to MetaCart
(Show Context)
We used mouse hepatic chromatin enriched with an FXR antibody and chromatin immunoprecipitation-sequencing (ChIP-seq) to evaluate FXR binding on a genome-wide scale. This identified 1656 FXR-binding sites and 10 % were located within 2 kb of a transcription start site which is much higher than predicted by random occurrence. A motif search uncovered a canonical nuclear receptor IR-1 site, consistent with in vitro DNA-binding studies reported previously. A separate nuclear receptor half-site for monomeric receptors such as LRH-1 was co-enriched and FXR activation of four newly identified promoters was significantly augmented by an LRH-1 expression vector in a co-transfection assay. There were 1038 genes located within 20 kb of a peak and a gene set enrichment analysis showed that genes identified by our ChIP-seq analysis are highly correlated with genes activated by an FXR-VP16 adenovirus in primary mouse hepatocytes providing functional relevance to the genome-wide binding study. Gene Ontology analysis showed FXR-binding sites close to many genes in lipid, fatty acid and steroid metabolism. Other broad gene clusters related to metabolism, transport, signaling and glycolysis were also significantly enriched. Thus, FXR may have a much wider role in cellular metabolism than previously appreciated.
Finding subtypes of transcription factor motif pairs with distinct regulatory roles
- Nucleic Acids Res
, 2011
"... with distinct regulatory roles ..."
(Show Context)
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data
- Bioinformatics
, 2009
"... ChIP-based high throughput data ..."
(Show Context)
Improved similarity scores for comparing motifs
- Bioinformatics
, 2011
"... Motivation: A question that often comes up after applying a motif finder to a set of co-regulated DNA sequences is whether the reported putative motif is similar to any known motif. While several tools have been designed for this task, Habib et al. (2008) pointed out that the scores that are commonl ..."
Abstract
-
Cited by 4 (0 self)
- Add to MetaCart
(Show Context)
Motivation: A question that often comes up after applying a motif finder to a set of co-regulated DNA sequences is whether the reported putative motif is similar to any known motif. While several tools have been designed for this task, Habib et al. (2008) pointed out that the scores that are commonly used for measuring similarity between motifs do not distinguish between a good alignment of two informative columns (say, all-A) and one of two uninformative columns. This observation explains why tools such as TOMTOM occasionally return an alignment of uninformative columns which is clearly spurious. To address this problem Habib et al. suggested a new score (BLiC) which uses a Bayesian information criterion to penalize matches that are also similar to the background distribution. Results: We show that the BLiC score exhibits other, highly undesirable properties, and we offer instead a general approach to adjust any motif similarity score so as to reduce the number of reported spurious alignments of uninformative columns. We implement our method in TOMTOM and show that, without significantly compromising TOMTOM’s retrieval accuracy or its runtime, we can drastically reduce the number of uninformative alignments. Availability and Implementation: The modified TOMTOM is available as part of the MEME Suite at
Contreras-Moreira B: The twilight zone of cis element alignments
- Nucleic Acids Res
"... Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the com-parison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed y ..."
Abstract
-
Cited by 4 (3 self)
- Add to MetaCart
(Show Context)
Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the com-parison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare
