Integrated analysis of motif activity and gene expression changes of transcription factors
出版年份 2017 全文链接
标题
Integrated analysis of motif activity and gene expression changes of transcription factors
作者
关键词
-
出版物
GENOME RESEARCH
Volume 28, Issue 2, Pages 243-255
出版商
Cold Spring Harbor Laboratory
发表日期
2017-12-13
DOI
10.1101/gr.227231.117
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
- (2017) Rasmus Siersbæk et al. MOLECULAR CELL
- Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data
- (2017) Mahdi Zamanighomi et al. NUCLEIC ACIDS RESEARCH
- Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility
- (2017) Xi Chen et al. NUCLEIC ACIDS RESEARCH
- TFBSTools: an R/bioconductor package for transcription factor binding site analysis
- (2016) Ge Tan et al. BIOINFORMATICS
- Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data
- (2016) Aleksander Jankowski et al. BIOINFORMATICS
- Modelingcis-regulation with a compendium of genome-wide histone H3K27ac profiles
- (2016) Su Wang et al. GENOME RESEARCH
- Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORγ Axis Regulating Proliferation in β Cells
- (2016) Søren Fisker Schmidt et al. Cell Reports
- E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data
- (2016) Min Kyung Kim et al. PLoS One
- BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
- (2015) Juhani Kähärä et al. BIOINFORMATICS
- Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data
- (2015) Michal Dabrowski et al. BMC BIOINFORMATICS
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon
- (2015) Hamed S Najafabadi et al. NATURE BIOTECHNOLOGY
- iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
- (2015) Jesper Grud Skat Madsen et al. NUCLEIC ACIDS RESEARCH
- KEGG as a reference resource for gene and protein annotation
- (2015) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
- (2015) Ivan V. Kulakovskiy et al. NUCLEIC ACIDS RESEARCH
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
- (2015) Socorro Gama-Castro et al. NUCLEIC ACIDS RESEARCH
- Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
- (2014) Matthew T. Weirauch et al. CELL
- ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- (2014) P. J. Balwierz et al. GENOME RESEARCH
- Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
- (2014) Richard I Sherwood et al. NATURE BIOTECHNOLOGY
- Gene Ontology Consortium: going forward
- (2014) NUCLEIC ACIDS RESEARCH
- AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors
- (2014) Hong-Mei Zhang et al. NUCLEIC ACIDS RESEARCH
- Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers
- (2014) Rasmus Siersbæk et al. Cell Reports
- Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network
- (2014) Carine Gubelmann et al. eLife
- Predicting tissue specific transcription factor binding sites
- (2013) Shan Zhong et al. BMC GENOMICS
- A community-driven global reconstruction of human metabolism
- (2013) Ines Thiele et al. NATURE BIOTECHNOLOGY
- Target analysis by integration of transcriptome and ChIP-seq data with BETA
- (2013) Su Wang et al. Nature Protocols
- Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
- (2013) P. Kheradpour et al. NUCLEIC ACIDS RESEARCH
- The Reactome pathway knowledgebase
- (2013) David Croft et al. NUCLEIC ACIDS RESEARCH
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- (2012) J. O. Yanez-Cuna et al. GENOME RESEARCH
- Sequence and chromatin determinants of cell-type-specific transcription factor binding
- (2012) A. Arvey et al. GENOME RESEARCH
- Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression
- (2012) M. S. Siersbaek et al. MOLECULAR AND CELLULAR BIOLOGY
- Fiji: an open-source platform for biological-image analysis
- (2012) Johannes Schindelin et al. NATURE METHODS
- TFClass: an expandable hierarchical classification of human transcription factors
- (2012) Edgar Wingender et al. NUCLEIC ACIDS RESEARCH
- Identification of New Genes Involved in Human Adipogenesis and Fat Storage
- (2012) Jörn Söhle et al. PLoS One
- Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology
- (2012) Brady Bernard et al. PLoS One
- FIMO: scanning for occurrences of a given motif
- (2011) Charles E. Grant et al. BIOINFORMATICS
- Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins
- (2011) Matthew Slattery et al. CELL
- Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis
- (2011) Rasmus Siersbaek et al. EMBO JOURNAL
- An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
- (2011) Eloi Mercier et al. PLoS One
- Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity
- (2011) Pernille Keller et al. BMC Endocrine Disorders
- Propagation of adipogenic signals through an epigenomic transition state
- (2010) D. J. Steger et al. GENES & DEVELOPMENT
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
- (2010) R. Pique-Regi et al. GENOME RESEARCH
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- Gene ontology analysis for RNA-seq: accounting for selection bias
- (2010) Matthew D Young et al. GENOME BIOLOGY
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Re-expression of GATA2 Cooperates with Peroxisome Proliferator-activated Receptor-γ Depletion to Revert the Adipocyte Phenotype
- (2009) Michael Schupp et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
- (2009) Harukazu Suzuki et al. NATURE GENETICS
- Adaptive Evolution in Zinc Finger Transcription Factors
- (2009) Ryan O. Emerson et al. PLoS Genetics
- Predicting the binding preference of transcription factors to individual DNA k-mers
- (2008) T. M. Alleyne et al. BIOINFORMATICS
- Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
- (2008) Michael F. Berger et al. CELL
- Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites
- (2008) Marcus B. Noyes et al. CELL
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started