Journal ArticleDOI
A General Framework for Weighted Gene Co-Expression Network Analysis
Bin Zhang,Steve Horvath +1 more
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TLDR
A general framework for `soft' thresholding that assigns a connection weight to each gene pair is described and several node connectivity measures are introduced and provided empirical evidence that they can be important for predicting the biological significance of a gene.Abstract:
Gene co-expression networks are increasingly used to explore the system-level functionality of genes. The network construction is conceptually straightforward: nodes represent genes and nodes are connected if the corresponding genes are significantly co-expressed across appropriately chosen tissue samples. In reality, it is tricky to define the connections between the nodes in such networks. An important question is whether it is biologically meaningful to encode gene co-expression using binary information (connected=1, unconnected=0). We describe a general framework for ;soft' thresholding that assigns a connection weight to each gene pair. This leads us to define the notion of a weighted gene co-expression network. For soft thresholding we propose several adjacency functions that convert the co-expression measure to a connection weight. For determining the parameters of the adjacency function, we propose a biologically motivated criterion (referred to as the scale-free topology criterion). We generalize the following important network concepts to the case of weighted networks. First, we introduce several node connectivity measures and provide empirical evidence that they can be important for predicting the biological significance of a gene. Second, we provide theoretical and empirical evidence that the ;weighted' topological overlap measure (used to define gene modules) leads to more cohesive modules than its ;unweighted' counterpart. Third, we generalize the clustering coefficient to weighted networks. Unlike the unweighted clustering coefficient, the weighted clustering coefficient is not inversely related to the connectivity. We provide a model that shows how an inverse relationship between clustering coefficient and connectivity arises from hard thresholding. We apply our methods to simulated data, a cancer microarray data set, and a yeast microarray data set.read more
Citations
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WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Journal ArticleDOI
The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova,Tikira Temu,Pavel Sinitcyn,Arthur Carlson,Marco Y. Hein,Tamar Geiger,Matthias Mann,Jürgen Cox +7 more
TL;DR: The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
Journal ArticleDOI
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
Kristin G. Ardlie,David S. DeLuca,Ayellet V. Segrè,Timothy J. Sullivan,Taylor Young,Ellen Gelfand,Casandra A. Trowbridge,Julian Maller,Taru Tukiainen,Monkol Lek,Lucas D. Ward,Pouya Kheradpour,Benjamin Iriarte,Yan Meng,Cameron D. Palmer,Tõnu Esko,Wendy Winckler,Joel N. Hirschhorn,Manolis Kellis,Daniel G. MacArthur,Gad Getz,Andrey A. Shabalin,Gen Li,Yi-Hui Zhou,Andrew B. Nobel,Ivan Rusyn,Fred A. Wright,Tuuli Lappalainen,Pedro G. Ferreira,Halit Ongen,Manuel A. Rivas,Alexis Battle,Sara Mostafavi,Jean Monlong,Michael Sammeth,Marta Melé,Ferran Reverter,Jakob M. Goldmann,Daphne Koller,Roderic Guigó,Mark I. McCarthy,Emmanouil T. Dermitzakis,Eric R. Gamazon,Hae Kyung Im,Anuar Konkashbaev,Dan L. Nicolae,Nancy J. Cox,Timothée Flutre,Xiaoquan Wen,Matthew Stephens,Jonathan K. Pritchard,Zhidong Tu,Bin Zhang,Tao Huang,Quan Long,Luan Lin,Jialiang Yang,Jun Zhu,Jun Liu,Amanda Brown,Bernadette Mestichelli,Denee Tidwell,Edmund Lo,Mike Salvatore,Saboor Shad,Jeffrey A. Thomas,John T. Lonsdale,Michael T. Moser,Bryan Gillard,Ellen Karasik,Kimberly Ramsey,Christopher Choi,Barbara A. Foster,John Syron,Johnell Fleming,Harold Magazine,Rick Hasz,Gary Walters,Jason Bridge,Mark Miklos,Susan L. Sullivan,Laura Barker,Heather M. Traino,Maghboeba Mosavel,Laura A. Siminoff,Dana R. Valley,Daniel C. Rohrer,Scott D. Jewell,Philip A. Branton,Leslie H. Sobin,Mary Barcus,Liqun Qi,Jeffrey McLean,Pushpa Hariharan,Ki Sung Um,Shenpei Wu,David Tabor,Charles Shive,Anna M. Smith,Stephen A. Buia,Anita H. Undale,Karna Robinson,Nancy Roche,Kimberly M. Valentino,Angela Britton,Robin Burges,Debra Bradbury,Kenneth W. Hambright,John Seleski,Greg E. Korzeniewski,Kenyon Erickson,Yvonne Marcus,Jorge Tejada,Mehran Taherian,Chunrong Lu,Margaret J. Basile,Deborah C. Mash,Simona Volpi,Jeffery P. Struewing,Gary F. Temple,Joy T. Boyer,Deborah Colantuoni,Roger Little,Susan E. Koester,Latarsha J. Carithers,Helen M. Moore,Ping Guan,Carolyn C. Compton,Sherilyn Sawyer,Joanne P. Demchok,Jimmie B. Vaught,Chana A. Rabiner,Nicole C. Lockhart +132 more
TL;DR: The landscape of gene expression across tissues is described, thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants are cataloged, complex network relationships are described, and signals from genome-wide association studies explained by eQTLs are identified.
Journal ArticleDOI
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
Luke Jostins,Stephan Ripke,Rinse K. Weersma,Richard H. Duerr,Dermot P.B. McGovern,Ken Y. Hui,James Lee,L. Philip Schumm,Yashoda Sharma,Carl A. Anderson,Jonah Essers,Mitja Mitrovic,Kaida Ning,Isabelle Cleynen,Emilie Theatre,Sarah L. Spain,Soumya Raychaudhuri,Philippe Goyette,Zhi Wei,Clara Abraham,Jean-Paul Achkar,Tariq Ahmad,Leila Amininejad,Ashwin N. Ananthakrishnan,Vibeke Andersen,Jane M. Andrews,Leonard Baidoo,Tobias Balschun,Peter A. Bampton,Alain Bitton,Gabrielle Boucher,Stephan Brand,Carsten Büning,Ariella Cohain,Sven Cichon,Mauro D'Amato,Dirk De Jong,Kathy L Devaney,Marla Dubinsky,Cathryn Edwards,David Ellinghaus,Lynnette R. Ferguson,Denis Franchimont,Karin Fransen,Richard B. Gearry,Michel Georges,Christian Gieger,Jürgen Glas,Talin Haritunians,Ailsa Hart,Christopher J. Hawkey,Matija Hedl,Xinli Hu,Tom H. Karlsen,Limas Kupčinskas,Subra Kugathasan,Anna Latiano,Debby Laukens,Ian C. Lawrance,Charlie W. Lees,Edouard Louis,Gillian Mahy,John C. Mansfield,Angharad R. Morgan,Craig Mowat,William G. Newman,Orazio Palmieri,Cyriel Y. Ponsioen,Uroš Potočnik,Natalie J. Prescott,Miguel Regueiro,Jerome I. Rotter,Richard K Russell,Jeremy D. Sanderson,Miquel Sans,Jack Satsangi,Stefan Schreiber,Lisa A. Simms,Jurgita Sventoraityte,Stephan R. Targan,Kent D. Taylor,Mark Tremelling,Hein W. Verspaget,Martine De Vos,Cisca Wijmenga,David C. Wilson,Juliane Winkelmann,Ramnik J. Xavier,Sebastian Zeissig,Bin Zhang,Clarence K. Zhang,Hongyu Zhao,Mark S. Silverberg,Vito Annese,Hakon Hakonarson,Steven R. Brant,Graham L. Radford-Smith,Christopher G. Mathew,John D. Rioux,Eric E. Schadt,Mark J. Daly,Andre Franke,Miles Parkes,Severine Vermeire,Jeffrey C. Barrett,Judy H. Cho +105 more
TL;DR: A meta-analysis of Crohn’s disease and ulcerative colitis genome-wide association scans is undertaken, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls.
Journal ArticleDOI
Synaptic, transcriptional and chromatin genes disrupted in autism
Silvia De Rubeis,Xin-Xin He,Arthur P. Goldberg,Christopher S. Poultney,Kaitlin E. Samocha,A. Ercument Cicek,Yan Kou,Li Liu,Menachem Fromer,Menachem Fromer,R. Susan Walker,Tarjinder Singh,Lambertus Klei,Jack A. Kosmicki,Shih-Chen Fu,Branko Aleksic,Monica Biscaldi,Patrick Bolton,Jessica M. Brownfeld,Jinlu Cai,Nicholas G. Campbell,Angel Carracedo,Angel Carracedo,Maria H. Chahrour,Andreas G. Chiocchetti,Hilary Coon,Emily L. Crawford,Lucy Crooks,Sarah Curran,Geraldine Dawson,Eftichia Duketis,Bridget A. Fernandez,Louise Gallagher,Evan T. Geller,Stephen J. Guter,R. Sean Hill,R. Sean Hill,Iuliana Ionita-Laza,Patricia Jiménez González,Helena Kilpinen,Sabine M. Klauck,Alexander Kolevzon,Irene Lee,Jing Lei,Terho Lehtimäki,Chiao-Feng Lin,Avi Ma'ayan,Christian R. Marshall,Alison L. McInnes,Benjamin M. Neale,Michael John Owen,Norio Ozaki,Mara Parellada,Jeremy R. Parr,Shaun Purcell,Kaija Puura,Deepthi Rajagopalan,Karola Rehnström,Abraham Reichenberg,Aniko Sabo,Michael Sachse,Stephen Sanders,Chad M. Schafer,Martin Schulte-Rüther,David Skuse,David Skuse,Christine Stevens,Peter Szatmari,Kristiina Tammimies,Otto Valladares,Annette Voran,Li-San Wang,Lauren A. Weiss,A. Jeremy Willsey,Timothy W. Yu,Timothy W. Yu,Ryan K. C. Yuen,Edwin H. Cook,Christine M. Freitag,Michael Gill,Christina M. Hultman,Thomas Lehner,Aarno Palotie,Aarno Palotie,Aarno Palotie,Gerard D. Schellenberg,Pamela Sklar,Matthew W. State,James S. Sutcliffe,Christopher A. Walsh,Christopher A. Walsh,Stephen W. Scherer,Michael E. Zwick,Jeffrey C. Barrett,David J. Cutler,Kathryn Roeder,Bernie Devlin,Mark J. Daly,Mark J. Daly,Joseph D. Buxbaum +99 more
TL;DR: Using exome sequencing, it is shown that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate of < 0.05, plus a set of 107 genes strongly enriched for those likely to affect risk (FDR < 0.30).
References
More filters
Journal ArticleDOI
Predicting gene function by conserved co-expression.
TL;DR: It is shown that gene co-expression, which generally provides only a very weak signal for the prediction of functional interactions, can provide a reliable signal by exploiting evolutionary conservation and using conservation between parallel duplicated gene pairs to predict function.
Journal ArticleDOI
Multiple roles of Rev3, the catalytic subunit of polζ in maintaining genome stability in vertebrates
Eiichiro Sonoda,Takashi Okada,Guang Yu Zhao,Satoshi Tateishi,Kasumi Araki,Masaru Yamaizumi,Takashi Yagi,Nicole S. Verkaik,Dik C. van Gent,Minoru Takata,Shunichi Takeda +10 more
TL;DR: Interestingly, REV3−/− cells showed reduced gene targeting efficiencies and significant increase in the level of chromosomal breaks in the subsequent M phase after IR in the G2 phase, suggesting the involvement of Rev3 in HR‐mediated double‐strand break repair.
Journal ArticleDOI
Large-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae
TL;DR: A genome-scale in silico model can be used to systematically reconcile existing data and fill in knowledge gaps about an organism to eliminate a number of false predictions and suggest a numberof experimentally testable hypotheses.
Journal ArticleDOI
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
Andrey Rzhetsky,Shawn M. Gomez +1 more
TL;DR: This work suggests a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks and generates networks that share important statistical properties with real molecular networks.
Journal ArticleDOI
Structure of a large social network.
Gábor Csányi,Balazs Szendroi +1 more
TL;DR: It is suggested that the double power law originates from two very different kinds of networks that are simultaneously present in the human social network.
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