Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TLDR
This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.Abstract:
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.read more
Citations
More filters
Book
Introduction to Data Mining for the Life Sciences
TL;DR: This book discusses data architecture and data modeling, machine learning techniques, and representation of data mining results in terms of input and output.
Journal ArticleDOI
The emergence and evolution of the research fronts in HIV/AIDS research.
David Fajardo-Ortiz,Malaquías López-Cervantes,Luis Duran,Michel Dumontier,Miguel Lara,Hector Ochoa,Victor M. Castano +6 more
TL;DR: Interestingly, the emergence of these fronts occurred in successive "waves" over the time which suggest a transition in the paradigmatic focus.
Journal ArticleDOI
How Many Protein-Protein Interactions Types Exist in Nature?
TL;DR: This study grouped the protein complexes in the protein data bank into 3,629 families and 1,761 folds, indicating that the current protein repository contains only 42% of quaternary folds in nature and a full coverage needs approximately a quarter century of experimental effort.
Journal ArticleDOI
mTOR-related neuropathology in mutant tsc2 zebrafish: Phenotypic, transcriptomic and pharmacological analysis.
Chloë Scheldeman,James D. Mills,Aleksandra Siekierska,Ines Serra,Daniëlle Copmans,Anand Iyer,Benjamin J. Whalley,Jan Willem Maes,Anna Jansen,Lieven Lagae,Eleonora Aronica,Peter de Witte +11 more
TL;DR: The phenotypic, transcriptomic and pharmacological analysis identified the tsc2-/- zebrafish as a preclinical model that mirrors well aspects of the human condition and delineated relevant TSC-related biological pathways.
Journal ArticleDOI
An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle
Priscila S. N. de Oliveira,Luiz Lehmann Coutinho,Polyana C. Tizioto,Aline Silva Mello Cesar,Gabriella B. Oliveira,Wellison Jarles da Silva Diniz,Andressa Oliveira de Lima,James M. Reecy,Gerson Barreto Mourão,Adhemar Zerlotini,Luciana Correia de Almeida Regitano +10 more
TL;DR: Findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
Summaries of Affymetrix GeneChip probe level data
Rafael A. Irizarry,Benjamin M. Bolstad,Francois Collin,Leslie Cope,Bridget G. Hobbs,Terence P. Speed,Terence P. Speed +6 more
TL;DR: It is found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models.
Related Papers (5)
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more