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Jaccard index based similarity measure to compare transcription factor binding site models

Ilya E Vorontsov, Ivan V Kulakovskiy, Vsevolod J Makeev
2013 Algorithms for Molecular Biology  
Conclusions: MACRO-APE can be effectively used to compute the Jaccard index based similarity for two TFBS models.  ...  PWM supplied with a score threshold defines a set of putative transcription factor binding sites (TFBS), thus providing a TFBS model.  ...  Background Transcription factors (TFs) with similar structures of their DNA binding domains often recognize similar transcription factor binding sites (TFBS).  ... 
doi:10.1186/1748-7188-8-23 pmid:24074225 pmcid:PMC3851813 fatcat:w4mezhr6xnatva7czmugss6iaa

SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures

Jens Lichtenberg, Laura Elnitski, David M Bodine, John Hancock
2017 Bioinformatics  
Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic  ...  SigSeeker has been validated using established benchmarks for transcription factor binding and histone modification ChIP-Seq data.  ...  Acknowledgements The authors would like to thank Valer Gotea, Gennady Margolin and Elisabeth Heuston for the many discussions relating to this work.  ... 
doi:10.1093/bioinformatics/btx276 pmid:28449120 pmcid:PMC5860059 fatcat:rwir7clzl5hzxoegxymms42vkm

Beware the Jaccard: the choice of metric is important and non-trivial in genomic colocalisation analysis [article]

Stefania Salvatore, Knut Dagestad Rand, Ivar Grytten, Egil Ferkingstad, Diana Eva Domanska, Lars Holden, Marius Gheorghe, Anthony Mathelier, Ingrid Glad, Geir Kjetil Sandve
2018 bioRxiv   pre-print
Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors.  ...  On both simulated and real genomic data, the Jaccard index is strongly affected by dataset size and should be used with caution.  ...  Acknowledgements We would like to thank Sveinung Gundersen for his invaluable help with creating the Galaxy page and instance for this specific project. Funding Not applicable.  ... 
doi:10.1101/479253 fatcat:7suvp3ttybeercdpdn65uui4xm

A METHODOLOGY FOR MOTIF DISCOVERY EMPLOYING ITERATED CLUSTER RE-ASSIGNMENT

Osman Abul, Finn Drabløs, Geir Kjetil Sandve
2006 Computational Systems Bioinformatics  
In this work, we propose a methodology for getting homogeregression paradigms based on iterative cluster re-assignment.  ...  INTRODUCTION Transcription Factors (TF) are proteins that selectively bind to short pieces (5-25nt long) of DNA, so called Transcription Factor Binding Sites (TFBS).  ...  To measure the cluster similarity between the true clustering and clusterings over iterations we measure the Jaccard index.  ... 
doi:10.1142/9781860947575_0032 fatcat:qfwklezfcbb2poqp75pqvmbepe

A METHODOLOGY FOR MOTIF DISCOVERY EMPLOYING ITERATED CLUSTER RE-ASSIGNMENT

Osman Abul, Finn Drabløs, Geir Kjetil Sandve
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
In this work, we propose a methodology for getting homogeregression paradigms based on iterative cluster re-assignment.  ...  INTRODUCTION Transcription Factors (TF) are proteins that selectively bind to short pieces (5-25nt long) of DNA, so called Transcription Factor Binding Sites (TFBS).  ...  To measure the cluster similarity between the true clustering and clusterings over iterations we measure the Jaccard index.  ... 
doi:10.1142/18609475730035 fatcat:aqly6t3mjjf4xhd65otfk6u3e4

A METHODOLOGY FOR MOTIF DISCOVERY EMPLOYING ITERATED CLUSTER RE-ASSIGNMENT

Osman Abul, Finn Drabløs, Geir Kjetil Sandve
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
In this work, we propose a methodology for getting homogeregression paradigms based on iterative cluster re-assignment.  ...  INTRODUCTION Transcription Factors (TF) are proteins that selectively bind to short pieces (5-25nt long) of DNA, so called Transcription Factor Binding Sites (TFBS).  ...  To measure the cluster similarity between the true clustering and clusterings over iterations we measure the Jaccard index.  ... 
doi:10.1142/1860947573_0035 fatcat:lj65lsd55rccfjaplt7doxbidy

Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells

Pengyi Yang, Andrew Oldfield, Taiyun Kim, Andrian Yang, Jean Yee Hwa Yang, Joshua W K Ho, Jonathan Wren
2017 Bioinformatics  
DNA binding proteins such as chromatin remodellers, transcription factors (TFs), histone modifiers and co-factors often bind cooperatively to activate or repress their target genes in a cell type-specific  ...  The comparison of co-localization sites to those bound by either BRG1 or CHD7 alone showed an enrichment of ESC master TFs binding and active chromatin architecture at co-localization sites.  ...  By ranking co-localization based on the delta Jaccard index, we also identified several other factors that show differential colocalization with BRG1.  ... 
doi:10.1093/bioinformatics/btx092 pmid:28203701 pmcid:PMC6248803 fatcat:znsciulqozhubebhj2oc62nfg4

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity

Kathleen Cheung, Matthew J. Barter, Julia Falk, Carole J. Proctor, Louise N. Reynard, David A. Young
2020 The FASEB Journal  
between cell-types compared to other chromatin states.  ...  Motif analysis revealed that the transcription factor SOX9 is enriched in chondrocyte enhancers.  ...  by the Jaccard similarity index.  ... 
doi:10.1096/fj.201902061rr pmid:32058623 fatcat:xfgtnicgojgzjo6mxcxqydcuny

Constructing tissue-specific transcriptional regulatory networks via a Markov random field

Shining Ma, Tao Jiang, Rui Jiang
2018 BMC Genomics  
Results: We propose a Markov random field (MRF) model for constructing tissue-specific transcriptional regulatory networks via integrative analysis of DNase-seq and RNA-seq data.  ...  on pairwise similarity between cell lines derived from gene expression data.  ...  Secondly, map these transcription factor binding sites to the promoter regions of genes and thus link TFs to target genes.  ... 
doi:10.1186/s12864-018-5277-6 fatcat:kwfzujs5qnev5agd2h4n5ofkla

Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding

Jasmin D Kurafeiski, Paulo Pinto, Erich Bornberg-Bauer, Josefa Gonzalez
2018 Genome Biology and Evolution  
In the case of transcription factor (TF) binding, both a novel TF and a novel-binding site would need to evolve concertedly.  ...  of TFs to TF-binding sites (TFBSs) affects the robustness and evolvability of this tightly regulated system.  ...  Set Distance Several measures can be implemented for the numerical assessment of the similarity of sets. One of those measures of similarity is the Jaccard Index.  ... 
doi:10.1093/gbe/evy269 pmid:30597011 pmcid:PMC6370388 fatcat:ceygyzm4frfkhphjzgmgynlpgm

Analysis of promoter regions of co-expressed genes identified by microarray analysis

Srinivas Veerla, Mattias Höglund
2006 BMC Bioinformatics  
transcription factor binding sites (TFBS) in co-expressed genes.  ...  In addition, we also found that 15% of the analyzed promoter regions contained transcription factors start sites for additional genes transcribed in the opposite direction.  ...  Hence, as the more commonly used similarity measures based on Euclidian distance or Pearson correlation would take shared absence of binding sites as a sign of similarity, these measures may produce misleading  ... 
doi:10.1186/1471-2105-7-384 pmid:16916454 pmcid:PMC1560170 fatcat:hkpnuzijxvd7fbfm635epandce

Analysis of Gene Regulatory Networks Inferred from ChIP-seq Data [chapter]

Eirini Stamoulakatou, Carlo Piccardi, Marco Masseroli
2019 Lecture Notes in Computer Science  
Computational network biology aims to understand cell behavior through complex network analysis.  ...  The Chromatin Immuno-Precipitation sequencing (ChIP-seq) technique allows interrogating the physical binding interactions between proteins and DNA using Next-Generation Sequencing.  ...  -The Jaccard index (J ), a statistic used for comparing the similarity of sample sets.  ... 
doi:10.1007/978-3-030-17938-0_29 fatcat:et6cxp4cd5aw3p76ixqcrvdmlm

Biological function derived from predicted structures in CASP11

Peter J. Huwe, Qifang Xu, Maxim V. Shapovalov, Vivek Modi, Mark D. Andrake, Roland L. Dunbrack
2016 Proteins: Structure, Function, and Bioinformatics  
Measures that evaluated similarity of contacts were reasonable for some of the models, although there was not a significant correlation with model accuracy.  ...  To accomplish this, we assessed the models for their ability to perform quantifiable tasks related to biological function.  ...  Acknowledgments We acknowledge funding from the NIH: R01 GM84453 to RLD and a Post-doctoral Trainee Fellowship, T32CA009035-38 to PJH.  ... 
doi:10.1002/prot.24997 pmid:27181425 pmcid:PMC4963311 fatcat:m5mvmv4vg5aqzc4p3o5kp53b2u

BEDTools: The Swiss-Army Tool for Genome Feature Analysis

Aaron R. Quinlan
2014 Current Protocols in Bioinformatics  
and transcription factor binding.  ...  Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression  ...  Work in this unit was supported by a grant to ARQ from the National Human Genome Research Institute: R01HG006693-01 (New algorithms and tools for large-scale genomic analysis).  ... 
doi:10.1002/0471250953.bi1112s47 pmid:25199790 pmcid:PMC4213956 fatcat:axkbt6pwi5d23d2cdidkekgsx4

Probing transcription factor combinatorics in different promoter classes and in enhancers

Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, Laurent Bréhélin
2019 BMC Genomics  
In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes.  ...  TFcoop aims to predict the binding sites of the target TF upon the nucleotide content of the sequences and of the binding affinity of all identified cooperating TFs.  ...  We are indebted to researchers around the globe who generated experimental data and made them freely available.  ... 
doi:10.1186/s12864-018-5408-0 fatcat:r7lgizsvujhjrknjrcuvxrie3m
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