Concepedia

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Jüri Reimand, Ruth Isserlin, Véronique Voisin, Mike Kucera, Christian Tannus-Lopes, Asha Rostamianfar, Lina Wadi, Mona Meyer, J. D. Wong, Changjiang Xu,

Nature Protocols · 2019 · 2.1K citations · 79 references

DOIFull text

Open access

Concepts

References

79

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

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha et al. · Proceedings of the National Academy of Sciences · 2005 · 56.7K citations · Full text

, , +12

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

Paul Shannon, Andrew Markiel, Owen Ozier et al. · Genome Research · 2003 · 54.3K citations · Full text

, , +17

Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith A. Blake et al. · Nature Genetics · 2000 · 44.6K citations · Full text

, , +9

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · Bioinformatics · 2009 · 44.5K citations · Full text

, , +14

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

Matthew E. Ritchie, Belinda Phipson, Di Wu et al. · Nucleic Acids Research · 2015 · 43K citations · Full text

, , +17