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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Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association.
Merry L. Lindsey,Manuel Mayr,Aldrin V. Gomes,Christian Delles,D. Kent Arrell,Anne M. Murphy,Richard A. Lange,Catherine E. Costello,Yufang Jin,Daniel T. Laskowitz,Flora Sam,Andre Terzic,Jennifer E. Van Eyk,Pothur R. Srinivas +13 more
TL;DR: This scientific statement is to summarize advances over this period that have catalyzed the capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field.
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Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity
TL;DR: Findings provide evidence that post-transcriptional studies of BRCA will benefit from transcending the one-locus-one-miRNA paradigm and taking into account all isoforms from each miRNA locus as well as the patient's race.
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SPATA2 links CYLD to the TNF‐α receptor signaling complex and modulates the receptor signaling outcomes
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Genetic architecture of plant stress resistance: multi‐trait genome‐wide association mapping
Manus P. M. Thoen,Nelson H. Davila Olivas,Karen J. Kloth,Silvia Coolen,Ping Ping Huang,Mark G. M. Aarts,Johanna A. Bac-Molenaar,Jaap Bakker,Harro J. Bouwmeester,Colette Broekgaarden,Colette Broekgaarden,Johan Bucher,Jacqueline Busscher-Lange,Xi Cheng,Emilie F. Fradin,Maarten A. Jongsma,Magdalena M. Julkowska,Joost J. B. Keurentjes,Wilco Ligterink,Corné M. J. Pieterse,Carolien Ruyter-Spira,Geert Smant,Christa Testerink,Björn Usadel,Joop J. A. van Loon,Johan A. Van Pelt,Casper van Schaik,Saskia C. M. Van Wees,Richard G. F. Visser,Roeland E. Voorrips,Ben Vosman,Dick Vreugdenhil,S. Warmerdam,G.L. Wiegers,Joost van Heerwaarden,Willem Kruijer,Fred A. van Eeuwijk,Marcel Dicke +37 more
TL;DR: This article investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions and found that plants appear to deploy broad-spectrum defensive mechanisms influencing multiple traits in response to combined stresses.
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Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium
Steven Reid,Emily J. Kay,Lisa J. Neilson,Anne Theres Henze,Jens Serneels,Ewan J. McGhee,Sandeep Dhayade,Colin Nixon,John B. G. Mackey,Alice Santi,Karthic Swaminathan,Dimitris Athineos,Vasileios Papalazarou,Francesca Patella,Álvaro Román-Fernández,Yasmin ElMaghloob,Juan Ramon Hernandez-Fernaud,Ralf H. Adams,Shehab Ismail,David M. Bryant,Manuel Salmerón-Sánchez,Laura M. Machesky,Leo M. Carlin,Karen Blyth,Massimiliano Mazzone,Sara Zanivan +25 more
TL;DR: It is found that stiffness‐induced CCN1 activates β‐catenin nuclear translocation and signaling and that this contributes to upregulate N‐cadherin levels on the surface of the endothelium, in vitro, which facilitates N‐ cadher in‐dependent cancer cell–endothelium interaction.
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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
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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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