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      Gene co-expression analysis for functional classification and gene–disease predictions

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          Abstract

          Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.

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          Most cited references 101

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          Statistical mechanics of complex networks

          Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical links. While traditionally these systems were modeled as random graphs, it is increasingly recognized that the topology and evolution of real networks is governed by robust organizing principles. Here we review the recent advances in the field of complex networks, focusing on the statistical mechanics of network topology and dynamics. After reviewing the empirical data that motivated the recent interest in networks, we discuss the main models and analytical tools, covering random graphs, small-world and scale-free networks, as well as the interplay between topology and the network's robustness against failures and attacks.
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            Error and attack tolerance of complex networks

            Many complex systems, such as communication networks, display a surprising degree of robustness: while key components regularly malfunction, local failures rarely lead to the loss of the global information-carrying ability of the network. The stability of these complex systems is often attributed to the redundant wiring of the functional web defined by the systems' components. In this paper we demonstrate that error tolerance is not shared by all redundant systems, but it is displayed only by a class of inhomogeneously wired networks, called scale-free networks. We find that scale-free networks, describing a number of systems, such as the World Wide Web, Internet, social networks or a cell, display an unexpected degree of robustness, the ability of their nodes to communicate being unaffected by even unrealistically high failure rates. However, error tolerance comes at a high price: these networks are extremely vulnerable to attacks, i.e. to the selection and removal of a few nodes that play the most important role in assuring the network's connectivity.
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              featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features

               ,  ,   (2013)
              Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
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                Author and article information

                Journal
                Brief Bioinform
                Brief. Bioinformatics
                bib
                Briefings in Bioinformatics
                Oxford University Press
                1467-5463
                1477-4054
                July 2018
                10 January 2017
                10 January 2017
                : 19
                : 4
                : 575-592
                Affiliations
                [1 ]Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
                [2 ]Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
                Author notes
                Corresponding authors: Sipko van Dam, Systems Genetics, Department of Genetics, UMCG HPC CB50, P.O. Box: 30001, 9700 RB Groningen, The Netherlands, Tel.: +31 50 361 72 29; Fax: +31 50 361 72 31; E-mail: sipkovandam@ 123456gmail.com
                João Pedro de Magalhães, Institute of Ageing and Chronic Disease, University of Liverpool, William Duncan Building, Room 281, 6 West Derby Street, Liverpool L7 8TX, United Kingdom, Tel.: +44 151 7954517; Fax: +44 151 795 8420; E-mail: jp@ 123456senescence.info
                Article
                bbw139
                10.1093/bib/bbw139
                6054162
                28077403
                079f45cb-83d1-4760-a29a-9a2d61ae38a4
                © The Author 2017. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Pages: 18
                Product
                Funding
                Funded by: UK Biotechnology and Biological Sciences Research Council 10.13039/501100000268
                Award ID: BB/K016741/1
                Funded by: European Research Council 10.13039/100010663
                Award ID: 637640
                Funded by: Organization for Scientific Research
                Award ID: 917.14.374
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