Benchmark and integration of resources for the estimation of human transcription factor activities

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

(2018) Daniel J B Clarke et al.   NUCLEIC ACIDS RESEARCH

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm

(2018) Hongxu Ding et al.   Nature Communications

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Identification of Three Early Phases of Cell-Fate Determination during Osteogenic and Adipogenic Differentiation by Transcription Factor Dynamics

(2017) Jeroen van de Peppel et al.   Stem Cell Reports

Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

(2016) Rezvan Ehsani et al.   BMC BIOINFORMATICS

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

(2016) Sushil Tripathi et al.   Database-The Journal of Biological Databases and Curation

Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

(2016) Abel Gonzalez-Perez   Genome Medicine

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

(2016) Nurcan Tuncbag et al.   PLoS Computational Biology

The pan-cancer pathological regulatory landscape

(2016) Matias M. Falco et al.   Scientific Reports

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   BIOPRESERVATION AND BIOBANKING

Targeting chromatin binding regulation of constitutively active AR variants to overcome prostate cancer resistance to endocrine-based therapies

(2015) Siu Chiu Chan et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

(2015) Robert Lesurf et al.   NUCLEIC ACIDS RESEARCH

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   Biopreservation and Biobanking

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Estimating the activity of transcription factors by the effect on their target genes

(2014) Theresa Schacht et al.   BIOINFORMATICS

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

Sets and intersections

(2014) Alexander Lex et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

(2012) M. Bleda et al.   NUCLEIC ACIDS RESEARCH

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Cell Cycle Gene Networks Are Associated with Melanoma Prognosis

(2012) Li Wang et al.   PLoS One

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcription Factor Encyclopedia

(2012) Dimas Yusuf et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2010) H. Kawaji et al.   NUCLEIC ACIDS RESEARCH

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

(2010) Ahmed Essaghir et al.   NUCLEIC ACIDS RESEARCH

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

(2009) J. Boros et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional control of human p53-regulated genes

(2008) Todd Riley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY