Graphite Web: web tool for gene set analysis exploiting pathway topology

Inhibition of JAK1, 2/STAT3 Signaling Induces Apoptosis, Cell Cycle Arrest, and Reduces Tumor Cell Invasion in Colorectal Cancer Cells

(2015) Hua Xiong et al.   NEOPLASIA

graphite - a Bioconductor package to convert pathway topology to gene network

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

NetWalker: a contextual network analysis tool for functional genomics

(2012) Kakajan Komurov et al.   BMC GENOMICS

Does interleukin-6 link explain the link between tumour necrosis, local and systemic inflammatory responses and outcome in patients with colorectal cancer?

(2012) Graeme J.K. Guthrie et al.   CANCER TREATMENT REVIEWS

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

(2012) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans

(2011) Lily Yan Wang et al.   Epigenetics

Toll-like receptor genes and their association with colon and rectal cancer development and prognosis

(2011) Martha L. Slattery et al.   INTERNATIONAL JOURNAL OF CANCER

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

(2011) A. Lan et al.   NUCLEIC ACIDS RESEARCH

Hypoxia-induced Jagged2 promotes breast cancer metastasis and self-renewal of cancer stem-like cells

(2011) F Xing et al.   ONCOGENE

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit

(2010) Dexter Duncan et al.   BMC BIOINFORMATICS

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Gene set enrichment analysis made simple

(2010) Rafael A Irizarry et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

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

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Role of Notch signaling in colorectal cancer

(2009) L. Qiao et al.   CARCINOGENESIS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments

(2008) Andreas Keller et al.   BMC BIOINFORMATICS

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

Gene-set analysis and reduction

(2008) I. Dinu et al.   BRIEFINGS IN BIOINFORMATICS

HIF-1α and HIF-2α have divergent roles in colon cancer

(2008) Takaaki Imamura et al.   INTERNATIONAL JOURNAL OF CANCER