Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, +8

Proceedings of the National Academy of Sciences

GeneticsGenomicsGene RecognitionBioinformatics DatabaseGene Expression Profiling +21

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Paul Shannon, Andrew Markiel, Owen Ozier, +6

Genome Research

Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith A. Blake, +17

Nature Genetics

Functional GenomicsEngineeringBioinformatics DatabaseBiological DatabaseMedicine +9

KEGG: Kyoto Encyclopedia of Genes and Genomes

Minoru Kanehisa

Nucleic Acids Research

KEGG: Kyoto Encyclopedia of Genes and Genomes

Hiroyuki Ogata, Susumu Goto, Kazushige Sato, +3

Nucleic Acids Research

GeneticsMolecular BiologyGenomicsBioinformatics DatabaseKyoto Encyclopedia +16

Clustering by Passing Messages Between Data Points

Brendan J. Frey, Delbert Dueck

Science

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl, +7

Bioinformatics

An automated method for finding molecular complexes in large protein interaction networks

Gary D. Bader, Christopher W.V. Hogue

BMC Bioinformatics

EngineeringInteractomicsNatural SciencesBiological NetworkComputational Biology +9

Lethality and centrality in protein networks

Hawoong Jeong, S. P. Mason, Albert-Ĺaszló Barabási, +1

Nature

BiologyNetwork ScienceEngineeringBiological NetworkComputational Biology +6

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Steven Maere, K. Heymans, Martin Kuiper

Computer applications in the biosciences