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
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Journal ArticleDOI
Gene expression signatures affected by alcohol-induced DNA methylomic deregulation in human embryonic stem cells.
Omar Khalid,Jeffrey J. Kim,Hyun-Sung Kim,Michael Hoang,Thanh G. Tu,Omid Elie,Connie Lee,Catherine Vu,Steve Horvath,Igor Spigelman,Yong Kim +10 more
TL;DR: A genome-wide analysis of EtOH's effects on the maintenance and differentiation of hESCs in culture revealed widespread EtOH-induced alterations with significant hypermethylation of many regions of chromosomes, helping in deciphering the precise mechanisms of alcohol-induced teratogenesis.
Journal ArticleDOI
Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells
Yinyin Chen,Kevin Huang,Martin N. Nakatsu,Zhigang Xue,Sophie X. Deng,Guoping Fan,Guoping Fan +6 more
TL;DR: This work profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells, and identified stage-specific markers associated with CEC development.
Journal ArticleDOI
EBV-miR-BART8-3p induces epithelial-mesenchymal transition and promotes metastasis of nasopharyngeal carcinoma cells through activating NF-κB and Erk1/2 pathways.
Cheng Lin,Jingfeng Zong,Wansong Lin,Minghui Wang,Yuanji Xu,Rui Zhou,Shaojun Lin,Qiaojuan Guo,Honglin Chen,Yunbin Ye,Bin Zhang,Jianji Pan +11 more
TL;DR: The present study demonstrates that EBV-miR-BART8-3p plays a significant role in inducing EMT and promoting metastasis through directly targeting RNF38 in NPC cells via the activation of NF-κB and Erk1/2 signaling pathways.
Journal ArticleDOI
Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores.
Heidi M. Appel,Howard W. Fescemyer,Juergen Ehlting,Juergen Ehlting,David J. Weston,Erin MacNeal Rehrig,Trupti Joshi,Dong Xu,Joerg Bohlmann,Jack C. Schultz +9 more
TL;DR: The hypothesis that Arabidopsis can recognize and respond differentially to insect species at the transcriptional level using a genome wide microarray is tested and transcriptional changes elicited by wounding and insects are heavily influenced by transcription factors.
Journal ArticleDOI
Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes
Michael V. Lombardo,Michael V. Lombardo,Tiziano Pramparo,Vahid H. Gazestani,Varun Warrier,Richard A. I. Bethlehem,Cynthia Carter Barnes,Linda Lopez,Nathan E. Lewis,Lisa T. Eyler,Lisa T. Eyler,Karen Pierce,Eric Courchesne +12 more
TL;DR: Large-scale associations between the leukocyte transcriptome and neural responses to speech in toddlers are found, and these associations differ between toddlers with ASD who have good versus poor language outcomes.
References
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