ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa (Q41958807)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24498971%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

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

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7 March 2020

0 references

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7 March 2020

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7 March 2020

Sergiu Netotea

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7 March 2020

David Sundell

series ordinal

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7 March 2020

language of work or name

English

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publication date

6 February 2014

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7 March 2020

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7 March 2020

volume

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7 March 2020

page(s)

106

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PLANEX: the plant co-expression database

7 March 2020

cites work

1 reference

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Evaluation of gene association methods for coexpression network construction and biological knowledge discovery

5 June 2018

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5 June 2018

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GraphAlignment: Bayesian pairwise alignment of biological networks.

5 June 2018

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Beyond differential expression: the quest for causal mutations and effector molecules

5 June 2018

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Integration of breast cancer gene signatures based on graph centrality

5 June 2018

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AlignNemo: a local network alignment method to integrate homology and topology

5 June 2018

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Comparative studies of gene expression and the evolution of gene regulation

5 June 2018

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Large-scale co-expression approach to dissect secondary cell wall formation across plant species

5 June 2018

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Comparative co-expression analysis in plant biology

5 June 2018

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PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction.

5 June 2018

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Comparing statistical methods for constructing large scale gene networks

5 June 2018

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Evolution of biological interaction networks: from models to real data

5 June 2018

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The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

5 June 2018

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The Pfam protein families database

5 June 2018

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Are there laws of genome evolution?

5 June 2018

1 reference

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PlaNet: combined sequence and expression comparisons across plant networks derived from seven species

5 June 2018

1 reference

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Human-specific loss of regulatory DNA and the evolution of human-specific traits

5 June 2018

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Measuring the evolutionary rewiring of biological networks

5 June 2018

1 reference

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A systems biology model of the regulatory network in Populusleaves reveals interacting regulators and conserved regulation

5 June 2018

1 reference

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COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Ten years of genetics and genomics: what have we achieved and where are we heading?

5 June 2018

1 reference

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agriGO: a GO analysis toolkit for the agricultural community

5 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Topological network alignment uncovers biological function and phylogeny

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

IsoRankN: spectral methods for global alignment of multiple protein networks

5 June 2018

1 reference

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Cross species analysis of microarray expression data

5 June 2018

1 reference

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A cross-species transcriptomics approach to identify genes involved in leaf development

5 June 2018

1 reference

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NCBI GEO: archive for high-throughput functional genomic data

5 June 2018

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Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus.

5 June 2018

1 reference

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Getting connected: analysis and principles of biological networks

5 June 2018

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Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

5 June 2018

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How to infer gene networks from expression profiles

5 June 2018

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

5 June 2018

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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

5 June 2018

1 reference

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Cross-species analysis of biological networks by Bayesian alignment

5 June 2018

1 reference

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Spontaneous evolution of modularity and network motifs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Conserved patterns of protein interaction in multiple species

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Bioconductor: open software development for computational biology and bioinformatics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

affy--analysis of Affymetrix GeneChip data at the probe level

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Network biology: understanding the cell's functional organization

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Mixing patterns in networks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Network motifs in the transcriptional regulation network of Escherichia coli

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Random graphs with arbitrary degree distributions and their applications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3925997

Gene ontology: tool for the unification of biology

5 June 2018

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Emergence of Scaling in Random Networks

5 June 2018

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Yeast microarrays for genome wide parallel genetic and gene expression analysis

5 June 2018

1 reference

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Quantitative monitoring of gene expression patterns with a complementary DNA microarray

5 June 2018

1 reference

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The evolutionary origins of modularity

5 June 2018

1 reference

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BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

18 August 2018

1 reference

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Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice

18 August 2018

1 reference

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Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms

18 August 2018

1 reference

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Evolutionary conservation of expression profiles between human and mouse orthologous genes.

18 August 2018

1 reference

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

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24498971

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-106

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24498971%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

7 March 2020

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-106

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24498971%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

PubMed publication ID

24498971

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24498971%20AND%20SRC:MED&resulttype=core&format=json