TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue 6, Pages e31-e31
Publisher
Oxford University Press (OUP)
Online
2017-12-19
DOI
10.1093/nar/gkx1279
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
- (2017) Runxuan Zhang et al. NUCLEIC ACIDS RESEARCH
- Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules
- (2017) Colin Ruprecht et al. PLANT JOURNAL
- Genome-wide characterization of differential transcript usage in Arabidopsis thaliana
- (2017) Dries Vaneechoutte et al. PLANT JOURNAL
- Predictive Models of Spatial Transcriptional Response to High Salinity
- (2017) Sahra Uygun et al. PLANT PHYSIOLOGY
- Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation
- (2017) Marian Bemer et al. TRENDS IN PLANT SCIENCE
- Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
- (2016) Ronan C. O’Malley et al. CELL
- Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors
- (2016) Erin E. Sparks et al. DEVELOPMENTAL CELL
- Near-optimal probabilistic RNA-seq quantification
- (2016) Nicolas L Bray et al. NATURE BIOTECHNOLOGY
- PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
- (2016) Jinpu Jin et al. NUCLEIC ACIDS RESEARCH
- Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
- (2016) Zefu Lu et al. NUCLEIC ACIDS RESEARCH
- Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation
- (2016) Miguel de Lucas et al. PLANT CELL
- A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling
- (2016) Anna V. Klepikova et al. PLANT JOURNAL
- New BAR tools for mining expression data and exploringCis-elements inArabidopsis thaliana
- (2016) Ryan S. Austin et al. PLANT JOURNAL
- A transcription factor hierarchy defines an environmental stress response network
- (2016) L. Song et al. SCIENCE
- Positional distribution of transcription factor binding sites in Arabidopsis thaliana
- (2016) Chun-Ping Yu et al. Scientific Reports
- Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics
- (2015) Diane G Burgess et al. CURRENT OPINION IN PLANT BIOLOGY
- Reassessing the “Duon” Hypothesis of Protein Evolution
- (2015) Ke Xing et al. MOLECULAR BIOLOGY AND EVOLUTION
- PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
- (2015) Chi-Nga Chow et al. NUCLEIC ACIDS RESEARCH
- Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses
- (2015) Pankaj Barah et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
- (2015) Anthony Mathelier et al. NUCLEIC ACIDS RESEARCH
- From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks
- (2015) Ying Li et al. TRENDS IN GENETICS
- Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
- (2014) Matthew T. Weirauch et al. CELL
- Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis
- (2014) Anne Pfeiffer et al. Molecular Plant
- An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation
- (2014) C. Tian et al. Molecular Systems Biology
- An Arabidopsis gene regulatory network for secondary cell wall synthesis
- (2014) M. Taylor-Teeples et al. NATURE
- PLAZA 3.0: an access point for plant comparative genomics
- (2014) Sebastian Proost et al. NUCLEIC ACIDS RESEARCH
- Inference of Transcriptional Networks inArabidopsisthrough Conserved Noncoding Sequence Analysis
- (2014) Jan Van de Velde et al. PLANT CELL
- A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana
- (2014) K. S. Heyndrickx et al. PLANT CELL
- Promoter-Based Integration in Plant Defense Regulation
- (2014) B. Li et al. PLANT PHYSIOLOGY
- Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis
- (2014) A. Para et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA-binding specificities of plant transcription factors and their potential to define target genes
- (2014) José M. Franco-Zorrilla et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
- (2014) Alessandra M. Sullivan et al. Cell Reports
- Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
- (2014) Alice Pajoro et al. GENOME BIOLOGY
- An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
- (2013) Annabelle Haudry et al. NATURE GENETICS
- Gene networks controllingArabidopsis thalianaflower development
- (2013) Diarmuid Seosamh Ó'Maoiléidigh et al. NEW PHYTOLOGIST
- From plant gene regulatory grids to network dynamics
- (2012) Maria Katherine Mejia-Guerra et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
- (2012) Stefanie De Bodt et al. NEW PHYTOLOGIST
- Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis
- (2012) W. Zhang et al. PLANT CELL
- Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants
- (2012) Laura Baxter et al. PLANT CELL
- Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis
- (2012) J. Liu et al. PLANT CELL
- Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources
- (2012) K. S. Heyndrickx et al. PLANT PHYSIOLOGY
- A stele-enriched gene regulatory network in the Arabidopsis root
- (2011) S. M. Brady et al. Molecular Systems Biology
- The sequence read archive: explosive growth of sequencing data
- (2011) Y. Kodama et al. NUCLEIC ACIDS RESEARCH
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
- (2011) Philippe Lamesch et al. NUCLEIC ACIDS RESEARCH
- Arabidopsis paves the way: genomic and network analyses in crops
- (2010) Thilia Ferrier et al. CURRENT OPINION IN BIOTECHNOLOGY
- CORNET: A User-Friendly Tool for Data Mining and Integration
- (2010) S. De Bodt et al. PLANT PHYSIOLOGY
- The 5′ untranslated region of the FAD3 mRNA is required for its translational enhancement at low temperature in Arabidopsis roots
- (2010) Chun-Tao Wang et al. PLANT SCIENCE
- Evaluation of seed storage-protein gene 5′ untranslated regions in enhancing gene expression in transgenic rice seed
- (2010) Wen Xian Liu et al. THEORETICAL AND APPLIED GENETICS
- PlnTFDB: updated content and new features of the plant transcription factor database
- (2009) Paulino Pérez-Rodríguez et al. NUCLEIC ACIDS RESEARCH
- Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks
- (2009) K. Vandepoele et al. PLANT PHYSIOLOGY
- PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
- (2008) Wen-Chi Chang et al. BMC GENOMICS
- UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
- (2008) D. E. Newburger et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now