(Q30000675)

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SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways

scientific article (publication date: 8 April 2014)

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SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways (English)

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author name string

Juan Yu

1

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Zhenhai Zhang

2

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Jiangang Wei

3

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Yi Ling

4

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Wenying Xu

5

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Zhen Su

6

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publication date

8 April 2014

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15

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1

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271

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Cytoscape

2 references

Europe PubMed Central

9 June 2022

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

based on heuristic

inferred from PubMed Central ID database lookup

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

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

1 reference

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21 May 2017

Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways

1 reference

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21 May 2017

LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes

1 reference

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21 May 2017

Genome sequence of the palaeopolyploid soybean

1 reference

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21 May 2017

PMRD: plant microRNA database

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21 May 2017

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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21 May 2017

Origin, biogenesis, and activity of plant microRNAs

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

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High-throughput functional annotation and data mining with the Blast2GO suite

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21 May 2017

The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max.

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21 May 2017

microRNA-directed phasing during trans-acting siRNA biogenesis in plants

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21 May 2017

Interdependency of brassinosteroid and auxin signaling in Arabidopsis

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MicroRNAs: genomics, biogenesis, mechanism, and function

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Microarray data normalization and transformation

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Prediction of plant microRNA targets

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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

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21 May 2017

The Arabidopsis thaliana TAG1 mutant has a mutation in a diacylglycerol acyltransferase gene

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A genome-wide association study of seed protein and oil content in soybean.

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3 June 2018

Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants

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3 June 2018

Acyl-lipid metabolism

1 reference

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3 June 2018

SoyProDB: A database for the identification of soybean seed proteins

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3 June 2018

Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.

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3 June 2018

psRNATarget: a plant small RNA target analysis server

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3 June 2018

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

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3 June 2018

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants

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3 June 2018

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

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3 June 2018

Mutant alleles of FAD2-1A and FAD2-1Bcombine to produce soybeans with the high oleic acid seed oil trait

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3 June 2018

Cytoscape Web: an interactive web-based network browser

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3 June 2018

agriGO: a GO analysis toolkit for the agricultural community

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3 June 2018

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Prediction of novel miRNAs and associated target genes in Glycine max.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

SoyDB: a knowledge database of soybean transcription factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

SoyBase, the USDA-ARS soybean genetics and genomics database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Nanoridges that characterize the surface morphology of flowers require the synthesis of cutin polyester

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Soybean oil: genetic approaches for modification of functionality and total content

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families

1 reference

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3 June 2018

Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules

1 reference

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3 June 2018

ATTED-II provides coexpressed gene networks for Arabidopsis

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3 June 2018

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Functional symmetry of the B3 network controlling seed development

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3 June 2018

SoyXpress: a database for exploring the soybean transcriptome

1 reference

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3 June 2018

Reconstituting plant miRNA biogenesis

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Novel and nodulation-regulated microRNAs in soybean roots.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Identification of acyltransferases required for cutin biosynthesis and production of cutin with suberin-like monomers.

1 reference

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3 June 2018

An Arabidopsis gene network based on the graphical Gaussian model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Reverse engineering cellular networks.

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3 June 2018

Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Bayesian network analysis of signaling networks: a primer

1 reference

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3 June 2018

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1 reference

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3 June 2018

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3 June 2018

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3 June 2018

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1 reference

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3 June 2018

The microarray explorer tool for data mining of cDNA microarrays: application for the mammary gland

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Plant cis-acting regulatory DNA elements (PLACE) database: 1999

1 reference

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3 June 2018

Oleosins and oil bodies in seeds and other organs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Gene expression during plant embryogenesis and germination: an overview

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Tetramer of a 21-base pair synthetic element confers seed expression and transcriptional enhancement in response to water stress and abscisic acid.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

3 June 2018

Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Soybean oil biosynthesis: role of diacylglycerol acyltransferases.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Expression of Umbelopsis ramanniana DGAT2A in seed increases oil in soybean.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

DGAT1, DGAT2 and PDAT expression in seeds and other tissues of epoxy and hydroxy fatty acid accumulating plants

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Vernonia DGATs increase accumulation of epoxy fatty acids in oil.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Identification and characterization of new plant microRNAs using EST analysis.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Conservation and divergence of plant microRNA genes.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Identification of soybean microRNAs and their targets

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Application of cDNA microarrays to examine gene expression differences in schizophrenia

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

A phenylalanine in DGAT is a key determinant of oil content and composition in maize

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Analysis of acyl fluxes through multiple pathways of triacylglycerol synthesis in developing soybean embryos.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Regulation of abscisic acid-induced transcription

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-271

21 January 2018

An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

26 November 2018

Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4051163

26 November 2018

The TAG1 locus of Arabidopsis encodes for a diacylglycerol acyltransferase

1 reference

https://pubmed.ncbi.nlm.nih.gov/24712981

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics

1 reference

https://pubmed.ncbi.nlm.nih.gov/24712981

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The acyltransferase GPAT5 is required for the synthesis of suberin in seed coat and root of Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/24712981

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Alteration of seed fatty acid composition by an ethyl methanesulfonate-induced mutation in Arabidopsis thaliana affecting diacylglycerol acyltransferase activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/24712981

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds

1 reference

https://pubmed.ncbi.nlm.nih.gov/24712981

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2164-15-271

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Dimensions Publication ID

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-271

release_mqyjhtoaq5durli2ikqwnela6a

1 reference

https://api.fatcat.wiki/v0/release/mqyjhtoaq5durli2ikqwnela6a

24 November 2022

based on heuristic

mapped directly with Wikidata item

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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