Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes

(2016) Vicente Martínez-Redondo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

A Network of Splice Isoforms for the Mouse

(2016) Hong-Dong Li et al.   Scientific Reports

Lmod2 piggyBac mutant mice exhibit dilated cardiomyopathy

(2016) Shuang Li et al.   Cell and Bioscience

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering

(2016) Chuan Gao et al.   PLoS Computational Biology

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Knockout of Lmod2 results in shorter thin filaments followed by dilated cardiomyopathy and juvenile lethality

(2015) Christopher T. Pappas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse

(2015) Hong-Dong Li et al.   Database-The Journal of Biological Databases and Curation

A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition

(2015) Jerneja Tomsic et al.   Scientific Reports

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

(2015) Emma Pierson et al.   PLoS Computational Biology

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

(2015) Christopher DeBoever et al.   PLoS Computational Biology

Novel Distal eQTL Analysis Demonstrates Effect of Population Genetic Architecture on Detecting and Interpreting Associations

(2014) M. Weiser et al.   GENETICS

The discovery of integrated gene networks for autism and related disorders

(2014) Fereydoun Hormozdiari et al.   GENOME RESEARCH

The adipogenic transcriptional cofactor ZNF638 interacts with splicing regulators and influences alternative splicing

(2014) Chen Du et al.   JOURNAL OF LIPID RESEARCH

Ensemble-Based Network Aggregation Improves the Accuracy of Gene Network Reconstruction

(2014) Rui Zhong et al.   PLoS One

Multi-tissue Analysis of Co-expression Networks by Higher-Order Generalized Singular Value Decomposition Identifies Functionally Coherent Transcriptional Modules

(2014) Xiaolin Xiao et al.   PLoS Genetics

TBX3 Regulates Splicing In Vivo: A Novel Molecular Mechanism for Ulnar-Mammary Syndrome

(2014) Pavan Kumar P. et al.   PLoS Genetics

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing

(2013) S Mostafavi et al.   MOLECULAR PSYCHIATRY

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method

(2013) Wenyuan Li et al.   NUCLEIC ACIDS RESEARCH

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

(2013) Sara Mostafavi et al.   PLoS One

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrating many co-splicing networks to reconstruct splicing regulatory modules

(2012) Chao Dai et al.   BMC Systems Biology

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Mab21l2 Is Essential for Embryonic Heart and Liver Development

(2012) Yohei Saito et al.   PLoS One

RBM25/LUC7L3 Function in Cardiac Sodium Channel Splicing Regulation of Human Heart Failure

(2012) Ge Gao et al.   TRENDS IN CARDIOVASCULAR MEDICINE

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Variants Affecting Exon Skipping Contribute to Complex Traits

(2012) Younghee Lee et al.   PLoS Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction

(2011) Rosario Michael Piro et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Understanding splicing regulation through RNA splicing maps

(2011) Joshua T. Witten et al.   TRENDS IN GENETICS

Systems genetics for drug target discovery

(2011) Nadia M. Penrod et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The exon junction complex component Magoh controls brain size by regulating neural stem cell division

(2010) Debra L Silver et al.   NATURE NEUROSCIENCE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

The pathobiology of splicing

(2009) Amanda J Ward et al.   JOURNAL OF PATHOLOGY

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

(2009) Mo Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

Alternative Splicing and Tumor Progression

(2008) Claudia Ghigna et al.   CURRENT GENOMICS

Novel Splicing Factor RBM25 Modulates Bcl-x Pre-mRNA 5' Splice Site Selection

(2008) A. Zhou et al.   MOLECULAR AND CELLULAR BIOLOGY

HBP21: A Novel Member of TPR Motif Family, as a Potential Chaperone of Heat Shock Protein 70 in Proliferative Vitreoretinopathy (PVR) and Breast Cancer

(2008) Qinghuai Liu et al.   MOLECULAR BIOTECHNOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles

(2008) Carlos Prieto et al.   PLoS One

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA