Journal ArticleDOI
A General Framework for Weighted Gene Co-Expression Network Analysis
Bin Zhang,Steve Horvath +1 more
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
More filters
Journal ArticleDOI
Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients
Yafei Li,Hui Tang,Zhifu Sun,Aaron O. Bungum,Eric S. Edell,Wilma L. Lingle,Shawn M. Stoddard,Mingrui Zhang,Jin Jen,Ping Yang,Liang Wang,Liang Wang +11 more
TL;DR: The results suggest that a network-based approach may facilitate discovery of key genes that are closely linked to survival in patients with lung adenocarcinoma.
Journal ArticleDOI
Parallel mRNA and microRNA profiling of HEV71-infected human neuroblastoma cells reveal the up-regulation of miR-1246 in association with DLG3 repression.
Li-Juan Xu,Tao Jiang,Wei Zhao,Jian-Feng Han,Juan Liu,Yong-Qiang Deng,Shun-Ya Zhu,Yue-Xiang Li,Qing-Gong Nian,Yu Zhang,Wu Xiaoyan,E-De Qin,Cheng-Feng Qin +12 more
TL;DR: Detailed miRNA expression profiling in HEV71-infected human neuroblastoma SH-SY5Y cells suggested that miR-1246 might play a role in neurological pathogenesis ofHEV71 by regulating DLG3 gene in infected cells.
Journal ArticleDOI
Interactional and functional centrality in transcriptional co-expression networks
TL;DR: An original network centrality measure, called annotation transcriptional centrality (ATC) computed by integrating gene expression profiles from microarray experiments with biological knowledge extracted from public genomic databases is presented.
Journal ArticleDOI
Fruits from ripening impaired, chlorophyll degraded and jasmonate insensitive tomato mutants have altered tocopherol content and composition.
Juliana Almeida,Ramón Asis,Virginia Noel Molineri,Ivan Sestari,Bruno Silvestre Lira,Fernando Carrari,Lázaro Eustáquio Pereira Peres,Magdalena Rossi +7 more
TL;DR: Transcriptional profiles from fruits of ripening and senescence-related tomato mutants suggested that maintenance of the de novo phytyl diphosphate synthesis might, in later ripening stages, compensate for the lack of chlorophyll-derived phytol used in tocopherol production.
Journal ArticleDOI
Functional Module Analysis for Gene Coexpression Networks with Network Integration
TL;DR: An effective method for module identification from multiple networks under different conditions is developed and the main functions of most modules for the corresponding disease have been addressed by other researchers, which may provide the theoretical basis for further studying the modules experimentally.
References
More filters
Journal ArticleDOI
Emergence of Scaling in Random Networks
TL;DR: A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
Journal ArticleDOI
Statistical mechanics of complex networks
TL;DR: In this paper, a simple model based on the power-law degree distribution of real networks was proposed, which was able to reproduce the power law degree distribution in real networks and to capture the evolution of networks, not just their static topology.
Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Book
Finding Groups in Data: An Introduction to Cluster Analysis
TL;DR: An electrical signal transmission system, applicable to the transmission of signals from trackside hot box detector equipment for railroad locomotives and rolling stock, wherein a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count.
Journal ArticleDOI
R: A Language for Data Analysis and Graphics
Ross Ihaka,Robert Gentleman +1 more
TL;DR: In this article, the authors discuss their experience designing and implementing a statistical computing language, which combines what they felt were useful features from two existing computer languages, and they feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scope.
Related Papers (5)
WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
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