Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis

Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation

(2015) Benjamin R. Sabari et al.   MOLECULAR CELL

The prognostic impact of lipid biosynthesis-associated markers, HSD17B2 and HMGCS2, in rectal cancer treated with neoadjuvant concurrent chemoradiotherapy

(2015) Ying-En Lee et al.   TUMOR BIOLOGY

TRRUST: a reference database of human transcriptional regulatory interactions

(2015) Heonjong Han et al.   Scientific Reports

Tumor suppression by miR-26 overrides potential oncogenic activity in intestinal tumorigenesis

(2014) Lauren R. Zeitels et al.   GENES & DEVELOPMENT

An evaluation and replication of miRNAs with disease stage and colorectal cancer-specific mortality

(2014) Martha L. Slattery et al.   INTERNATIONAL JOURNAL OF CANCER

High KLF4 level in normal tissue predicts poor survival in colorectal cancer patients

(2014) Ha-young Lee et al.   World Journal of Surgical Oncology

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Both STAT1 and STAT3 are favourable prognostic determinants in colorectal carcinoma

(2013) C Gordziel et al.   BRITISH JOURNAL OF CANCER

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

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

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

(2011) L. Geistlinger et al.   BIOINFORMATICS

Clinical Significance of Osteoprotegerin Expression in Human Colorectal Cancer

(2011) S. Tsukamoto et al.   CLINICAL CANCER RESEARCH

KLF4 Expression Correlates with the Degree of Differentiation in Colorectal Cancer

(2011) Ruolei Hu et al.   Gut and Liver

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Multiple Mechanisms Downstream of TLR-4 Stimulation Allow Expression of NKG2D Ligands To Facilitate Macrophage/NK Cell Crosstalk

(2010) P. Eissmann et al.   JOURNAL OF IMMUNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

An NF-κB–Dependent Role for JunB in the Induction of Proinflammatory Cytokines in LPS-Activated Bone Marrow–Derived Dendritic Cells

(2010) Tiphanie Gomard et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

DIANA-microT web server: elucidating microRNA functions through target prediction

(2009) M. Maragkakis et al.   NUCLEIC ACIDS RESEARCH

Induction and regulatory function of miR-9 in human monocytes and neutrophils exposed to proinflammatory signals

(2009) F. Bazzoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH