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
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Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation
Chunhe Li,Jin Wang,Jin Wang +2 more
TL;DR: Non-adiabaticity leads to more differentiated cell types and provides a natural explanation for the heterogeneity observed in the experiments and is found to be the optimal speeds of these cell fate decision-making processes.
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Identification of gene modules associated with drought response in rice by network-based analysis.
TL;DR: This study used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets and observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties.
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Mertk on tumor macrophages is a therapeutic target to prevent tumor recurrence following radiation therapy
Marka R. Crittenden,Jason R. Baird,David J. Friedman,Talicia Savage,Lauren Uhde,Alejandro F Alice,Benjamin Cottam,Kristina H. Young,Pippa Newell,Cynthia Nguyen,Shelly Bambina,Gwen Kramer,Emmanuel T. Akporiaye,Anna Malecka,Andrew Jackson,Michael J. Gough +15 more
TL;DR: It is demonstrated that the macrophage-specific phagocytic receptor, Mertk is upregulated in macrophages in the tumor following radiation therapy, and is a highly specific target whose absence permits tumor control in combination with radiation therapy.
Journal ArticleDOI
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis.
Fred Y. Peng,Randall J. Weselake +1 more
TL;DR: Genes involved in the accumulation of seed storage reserves are expressed in distinct patterns and regulated by different TFs, and promoter motifs for LEC1, DOF, GATA, and MYB transcription factors, as well as SORLIP5, are overrepresented in the promoter regions of fatty acid biosynthetic genes.
Journal ArticleDOI
Comparative gene expression profiling identifies common molecular signatures of NF-κB activation in canine and human diffuse large B cell lymphoma (DLBCL).
Manikhandan Mudaliar,D. Ross Haggart,Gino Miele,Grant Sellar,Karen A. L. Tan,John R. Goodlad,Elspeth Milne,David M. Vail,Ilene D. Kurzman,Daniel Crowther,David J. Argyle +10 more
TL;DR: The analysis demonstrated that for both human and canine DLBCL there is activation of the NF-κB/p65 canonical pathway, indicating that canine lymphoma could be used as a model to study NF-σκB-targeted therapeutics for human lymphoma.
References
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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.
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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.
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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.
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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.
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Gene Ontology: tool for the unification of biology
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