Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq (Q28651703)

April 2022 Public Data File from Crossref

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describes a project that uses

Cytoscape

object named as

Cytoscape

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Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

WGCNA

object named as

WGCNA

R package WGCNA

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

0 references

1 reference

Cellulose synthase complexes: composition and regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Dynamic changes in transcripts during regeneration of the secondary vascular system in Populus tomentosa Carr. revealed by cDNA microarrays

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

TopHat: discovering splice junctions with RNA-Seq

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Mapping and quantifying mammalian transcriptomes by RNA-Seq

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Multiple, distinct isoforms of sucrose synthase in pea

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

A general framework for weighted gene co-expression network analysis

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Coactivator and corepressor complexes in nuclear receptor function

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

A travel guide to Cytoscape plugins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Functional characterization of the poplar R2R3-MYB transcription factor PtoMYB216 involved in the regulation of lignin biosynthesis during wood formation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Modeling transcriptional networks regulating secondary growth and wood formation in forest trees

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

DNA-binding domains of plant-specific transcription factors: structure, function, and evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Gibberellin is required for the formation of tension wood and stem gravitropism in Acacia mangium seedlings.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Reprogramming of gene expression during compression wood formation in pine: coordinated modulation of S-adenosylmethionine, lignin and lignan related genes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis thaliana

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

EST analysis of functional genes associated with cell wall biosynthesis and modification in the secondary xylem of the yellow poplar (Liriodendron tulipifera) stem during early stage of tension wood formation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Transcriptional networks for lignin biosynthesis: more complex than we thought?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

An overview of the role of molecular chaperones in protein homeostasis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

The actin multigene family in Populus: organization, expression and phylogenetic analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

agriGO: a GO analysis toolkit for the agricultural community

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

3 June 2018

Wood formation in trees.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372042

Molecular cloning of 4-coumarate:coenzyme A ligase in loblolly pine and the roles of this enzyme in the biosynthesis of lignin in compression wood

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Suppression of 4-coumarate-CoA ligase in the coniferous gymnosperm Pinus radiata

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Xylem-specific and tension stress-responsive coexpression of KORRIGAN endoglucanase and three secondary wall-associated cellulose synthase genes in aspen trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Identification and characterization of the Populus sucrose synthase gene family.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Evidence that sucrose loaded into the phloem of a poplar leaf is used directly by sucrose synthase associated with various beta-glucan synthases in the stem

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

Functional genomics and cell wall biosynthesis in loblolly pine

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

OVATE FAMILY PROTEIN4 (OFP4) interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12864-015-1390-Y

21 January 2018

1 reference

12 December 2020

Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics

1 reference

12 December 2020

The poplar MYB transcription factors, PtrMYB3 and PtrMYB20, are involved in the regulation of secondary wall biosynthesis

1 reference

12 December 2020

1 reference

12 December 2020

10.1186/S12864-015-1390-Y

Identifiers

DOI

1 reference

Dimensions Publication ID

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s12864-015-1390-y

1 reference

1 reference

PubMed publication ID

25886950

1 reference