4.3 Review

Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression data

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Plant Sciences

Tools of the trade: studying molecular networks in plants

Sebastian Proost et al.

CURRENT OPINION IN PLANT BIOLOGY (2016)

Article Plant Sciences

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

Oren Tzfadia et al.

FRONTIERS IN PLANT SCIENCE (2016)

Review Plant Sciences

Learning from Co-expression Networks: Possibilities and Challenges

Elise A. R. Serin et al.

FRONTIERS IN PLANT SCIENCE (2016)

Article Biochemical Research Methods

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

S. Ballouz et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

Patrick T. Ryan et al.

BMC GENOMICS (2015)

Article Biotechnology & Applied Microbiology

Identification of crucial genes in intracranial aneurysm based on weighted gene coexpression network analysis

X. Zheng et al.

CANCER GENE THERAPY (2015)

Article Biochemical Research Methods

Prediction of Gene Co-Expression by Quantifying Heterogeneous Features

Abbasali Emamjomeh et al.

CURRENT BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

Zhi-Ping Liu

CURRENT GENOMICS (2015)

Article Biochemistry & Molecular Biology

GeneFriends: a human RNA-seq-based gene and transcript co-expression database

Sipko van Dam et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

ImmuCo: a database of gene co-expression in immune cells

Pingzhang Wang et al.

NUCLEIC ACIDS RESEARCH (2015)

Proceedings Paper Biophysics

Comparative analysis of co-expression networks reveals molecular changes during the cancer progression

P. Khosravi et al.

WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING, 2015, VOLS 1 AND 2 (2015)

Article Biochemical Research Methods

Reconstruction of gene co-expression network from microarray data using local expression patterns

Swarup Roy et al.

BMC BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding

Arun Kommadath et al.

BMC GENOMICS (2014)

Article Biotechnology & Applied Microbiology

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

Sergiu Netotea et al.

BMC GENOMICS (2014)

Article Biotechnology & Applied Microbiology

Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits

Maxime Rotival et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2014)

Article Biology

Review on statistical methods for gene network reconstruction using expression data

Y. X. Rachel Wang et al.

JOURNAL OF THEORETICAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

Hari Krishna Yalamanchili et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Plant Sciences

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

Takeshi Obayashi et al.

PLANT AND CELL PHYSIOLOGY (2014)

Article Biochemistry & Molecular Biology

Coexpression network analysis associated with call of rice seedlings for encountering heat stress

Neelam K. Sarkar et al.

PLANT MOLECULAR BIOLOGY (2014)

Article Multidisciplinary Sciences

Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

Denise M. Wolf et al.

PLOS ONE (2014)

Proceedings Paper Computer Science, Theory & Methods

A Clustering Based Method Accelerating Gene Regulatory Network Reconstruction

Georgios N. Dimitrakopoulos et al.

2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE (2014)

Article Biochemical Research Methods

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

Federico M. Giorgi et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

Darren C. J. Wong et al.

BMC GENOMICS (2013)

Article Plant Sciences

PLANEX: the plant co-expression database

Won Cheol Yim et al.

BMC PLANT BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

Liliana Lopez-Kleine et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2013)

Article Biochemistry & Molecular Biology

Stress induces remodelling of yeast interaction and co-expression networks

Sonja Lehtinen et al.

MOLECULAR BIOSYSTEMS (2013)

Article Biochemistry & Molecular Biology

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

Takeshi Obayashi et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Canonical correlation analysis for RNA-seq co-expression networks

Shengjun Hong et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Mathematical & Computational Biology

Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics

Jie Xiong et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2013)

Article Biotechnology & Applied Microbiology

DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis

Jun Li et al.

BIOMED RESEARCH INTERNATIONAL (2013)

Article Biochemical Research Methods

SNPxGE2: a database for human SNP-coexpression associations

Yupeng Wang et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Utilizing RNA-Seq data for de novo coexpression network inference

Ovidiu D. Iancu et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

CGCDB: A web-based resource for the investigation of gene coexpression in CHO cell culture

Colin Clarke et al.

BIOTECHNOLOGY AND BIOENGINEERING (2012)

Article Biochemical Research Methods

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Danielle G. Lemay et al.

BMC BIOINFORMATICS (2012)

Article Biochemical Research Methods

Comparison of co-expression measures: mutual information, correlation, and model based indices

Lin Song et al.

BMC BIOINFORMATICS (2012)

Review Biochemical Research Methods

Metabolic network reconstruction: advances in in silico interpretation of analytical information

Ning Chen et al.

CURRENT OPINION IN BIOTECHNOLOGY (2012)

Review Plant Sciences

Towards understanding how molecular networks evolve in plants

Lee Chae et al.

CURRENT OPINION IN PLANT BIOLOGY (2012)

Article Biochemical Research Methods

Wisdom of crowds for robust gene network inference

Daniel Marbach et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Detecting overlapping protein complexes in protein-protein interaction networks

Tamas Nepusz et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

MAGNET: MicroArray Gene expression and Network Evaluation Toolkit

George C. Linderman et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Plant Sciences

Comparative co-expression analysis in plant biology

Sara Movahedi et al.

PLANT CELL AND ENVIRONMENT (2012)

Article Multidisciplinary Sciences

Comparing Statistical Methods for Constructing Large Scale Gene Networks

Jeffrey D. Allen et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

In silico method for modelling metabolism and gene product expression at genome scale

Joshua A. Lerman et al.

NATURE COMMUNICATIONS (2012)

Article Biochemical Research Methods

Fast and efficient dynamic nested effects models

Holger Froehlich et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

BiC: a web server for calculating bimodality of coexpression between gene and protein networks

George C. Linderman et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

Artem Lysenko et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

Jeff Skinner et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

COXPRESdb: a database to compare gene coexpression in seven model animals

Takeshi Obayashi et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Plant Sciences

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

Kazuki Hamada et al.

PLANT AND CELL PHYSIOLOGY (2011)

Article Multidisciplinary Sciences

Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial peptidoglycan sensing and immunity to bacterial infection

Roland Willmann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Detecting Novel Associations in Large Data Sets

David N. Reshef et al.

SCIENCE (2011)

Article Biochemical Research Methods

CoP: a database for characterizing co-expressed gene modules with biological information in plants

Yoshiyuki Ogata et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Interactional and functional centrality in transcriptional co-expression networks

Edi Prifti et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

geWorkbench: an open source platform for integrative genomics

Aris Floratos et al.

BIOINFORMATICS (2010)

Article Mathematical & Computational Biology

A general co-expression network-based approach to gene expression analysis: comparison and applications

Jianhua Ruan et al.

BMC SYSTEMS BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

Hugues Richard et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

Identifying functional modules using expression profiles and confidence-scored protein interactions

Igor Ulitsky et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Arabidopsis gene co-expression network and its functional modules

Linyong Mao et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

ATTED-II provides coexpressed gene networks for Arabidopsis

Takeshi Obayashi et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Plant Sciences

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Bjoern Usadel et al.

PLANT CELL AND ENVIRONMENT (2009)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Review Plant Sciences

Regulon organization of Arabidopsis

Wieslawa I. Mentzen et al.

BMC PLANT BIOLOGY (2008)

Article Biochemistry & Molecular Biology

GeneCAT - novel webtools that combine BLAST and co-expression analyses

Marek Mutwil et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Plant Sciences

CressExpress: A tool for large-scale mining of expression data from Arabidopsis

Vinodh Srinivasasainagendra et al.

PLANT PHYSIOLOGY (2008)

Article Biochemical Research Methods

Computing topological parameters of biological networks

Yassen Assenov et al.

BIOINFORMATICS (2008)

Review Cell Biology

Getting connected: analysis and principles of biological networks

Xiaowei Zhu et al.

GENES & DEVELOPMENT (2007)

Article Biochemical Research Methods

Inferring cellular networks - a review

Florian Markowetz et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis

Takeshi Obayashi et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Evolutionary Biology

Global similarity and local divergence in human and mouse gene co-expression networks

Panayiotis Tsaparas et al.

BMC EVOLUTIONARY BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Arabidopsis Co-expression Tool (ACT):: web server tools for microarray-based gene expression analysis

Iain W. Manfield et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens

Renata F. Ditt et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2006)

Article Biochemical Research Methods

ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context

AA Margolin et al.

BMC BIOINFORMATICS (2006)

Article Computer Science, Artificial Intelligence

Feature selection based on mutual information: Criteria of max-dependency, max-relevance, and min-redundancy

HC Peng et al.

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE (2005)

Article Biochemistry & Molecular Biology

From single genes to co-expression networks: extracting knowledge from barley functional genomics

P Faccioli et al.

PLANT MOLECULAR BIOLOGY (2005)

Article Biotechnology & Applied Microbiology

Discovery of biological networks from diverse functional genomic data

Chad L. Myers et al.

GENOME BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Enhancer trapping identifies TRI, an Arabidopsis gene up-regulated by pathogen infection

I Fridborg et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2004)

Article Multidisciplinary Sciences

Genomic analysis of regulatory network dynamics reveals large topological changes

NM Luscombe et al.

NATURE (2004)

Article Biochemical Research Methods

CSB.DB: a comprehensive systems-biology database

D Steinhauser et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Coexpression analysis of human genes across many microarray data sets

HK Lee et al.

GENOME RESEARCH (2004)

Article Multidisciplinary Sciences

A gene-coexpression network for global discovery of conserved genetic modules

JM Stuart et al.

SCIENCE (2003)

Article Multidisciplinary Sciences

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)

OG Troyanskaya et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemical Research Methods

An automated method for finding molecular complexes in large protein interaction networks

GD Bader et al.

BMC BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Multidisciplinary Sciences

Transitive functional annotation by shortest-path analysis of gene expression data

XH Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemical Research Methods

The mutual information: Detecting and evaluating dependencies between variables

R Steuer et al.

BIOINFORMATICS (2002)

Article Cell Biology

Targets of AtWRKY6 regulation during plant senescence and pathogen defense

S Robatzek et al.

GENES & DEVELOPMENT (2002)

Article Multidisciplinary Sciences

MAP kinase signalling cascade in Arabidopsis innate immunity

T Asai et al.

NATURE (2002)

Review Biochemical Research Methods

Genetic network inference: from co-expression clustering to reverse engineering

P D'haeseleer et al.

BIOINFORMATICS (2000)