(Q34759450)

4 August 2017

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study (English)

1 reference

4 August 2017

2

1 reference

4 August 2017

F Alex Feltus

1

1 reference

PubMed ID

23738693

4 August 2017

Scott M Gibson

series ordinal

3

1 reference

PubMed ID

23738693

4 August 2017

Melissa C Smith

series ordinal

4

1 reference

4 August 2017

5 June 2013

1 reference

4 August 2017

1 reference

4 August 2017

7

1 reference

4 August 2017

44

1 reference

https://scigraph.springernature.com/pub.10.1186/1752-0509-7-44

4 August 2017

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in 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=3679940

Evidence for network evolution in an Arabidopsis interactome map.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

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=3679940

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=3679940

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=3679940

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=3679940

A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

Co-expression analysis of metabolic pathways in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

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=3679940

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=3679940

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

An Arabidopsis gene network based on the graphical Gaussian model.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

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=3679940

KAAS: an automatic genome annotation and pathway reconstruction server

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

A novel functional module detection algorithm for protein-protein interaction 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=3679940

Conservation and evolution of gene coexpression networks in human and chimpanzee brains

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Integrating genetic and network analysis to characterize genes related to mouse weight

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Functional partitioning of yeast co-expression networks after genome duplication

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Gene connectivity, function, and sequence conservation: predictions from modular yeast 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=3679940

A systematic comparison and evaluation of biclustering methods for gene expression 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=3679940

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=3679940

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=3679940

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=3679940

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=3679940

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=3679940

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=3679940

AraCyc: a biochemical pathway database for Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

DAVID: Database for Annotation, Visualization, and Integrated Discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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=3679940

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=3679940

Biclustering of expression 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=3679940

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=3679940

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

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

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-44

A duplication growth model of gene expression networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-44

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/10.1186%2F1752-0509-7-44

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-44

Random matrix analysis of localization properties of gene coexpression network.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3679940

Link communities reveal multiscale complexity in networks

26 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-7-44

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/23738693

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Topological and Functional Discovery in a Gene Coexpression Meta-Network of Gastric Cancer

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23738693

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/23738693

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-7-44

1 reference

journals/bmcsb/FeltusFGS13

4 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

4 August 2017

1 reference

PubMed ID

23738693