(Q34586391)

3 August 2017

Massive-scale gene co-expression network construction and robustness testing using random matrix theory (English)

1 reference

3 August 2017

2

1 reference

3 August 2017

Scott M Gibson

1

1 reference

3 August 2017

Sven Isaacson

3

1 reference

3 August 2017

Feng Luo

4

1 reference

3 August 2017

Frank A Feltus

5

1 reference

3 August 2017

Melissa C Smith

6

1 reference

3 August 2017

language of work or name

English

0 references

publication date

7 February 2013

1 reference

3 August 2017

1 reference

3 August 2017

8

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3 August 2017

2

1 reference

3 August 2017

e55871

1 reference

Creative Commons Attribution 4.0 International

3 August 2017

start time

7 February 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Discriminative local subspaces in gene expression data for effective gene function prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

The Pfam protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

NCBI GEO: archive for functional genomics data sets--10 years on

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

TobEA: an atlas of tobacco gene expression from seed to senescence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Arabidopsis gene co-expression network and its functional modules.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Threshold selection in gene co-expression networks using spectral graph theory techniques

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Coexpression network based on natural variation in human gene expression reveals gene interactions and functions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

WGCNA: an R package for weighted correlation network analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

InterPro: the integrative protein signature database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Articulation of three core metabolic processes in Arabidopsis: fatty acid biosynthesis, leucine catabolism and starch metabolism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

The UCSC Genome Browser Database: 2008 update

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

KEGG for linking genomes to life and the environment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Approaches for extracting practical information from gene co-expression networks in plant biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

The TIGR Rice Genome Annotation Resource: improvements and new features

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Bioconductor: open software development for computational biology and bioinformatics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Coexpression analysis of human genes across many microarray data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Network biology: understanding the cell's functional organization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Random matrix approach to cross correlations in financial data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

The human genome browser at UCSC

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3567026

Adaptive quality-based clustering of gene expression profiles.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Towards patterns tree of gene coexpression in eukaryotic species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Gene co-expression network topology provides a framework for molecular characterization of cellular state

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Deterministic scale-free networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Transcriptional coordination of the metabolic network in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Link communities reveal multiscale complexity in networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

A Coefficient of Agreement for Nominal Scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0055871

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23409071

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conservation and coevolution in the scale-free human gene coexpression network

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23409071

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0055871

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference