ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants (Q30714199)

20 August 2017

ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants (English)

1 reference

20 August 2017

0 references

Yasunobu Okamura

2

0 references

Shu Tadaka

object named as

Shu Tadaka

4

0 references

author name string

Takeshi Obayashi

1

1 reference

20 August 2017

Satoshi Ito

3

1 reference

20 August 2017

Yuichi Aoki

5

1 reference

20 August 2017

Matsuyuki Shirota

6

1 reference

20 August 2017

Kengo Kinoshita

7

1 reference

20 August 2017

10 December 2013

1 reference

Plant and Cell Physiology

20 August 2017

1 reference

20 August 2017

55

1 reference

20 August 2017

1

1 reference

20 August 2017

e6

1 reference

PLANEX: the plant co-expression database

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

ArrayExpress update--trends in database growth and links to data analysis tools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Fast gapped-read alignment with Bowtie 2

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Phytozome: a comparative platform for green plant genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

The Sequence Read Archive: explosive growth of sequencing data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

OryzaExpress: an integrated database of gene expression networks and omics annotations in rice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Differential expression analysis for sequence count data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

CoP: a database for characterizing co-expressed gene modules with biological information in plants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

A scaling normalization method for differential expression analysis of RNA-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Food security: the challenge of feeding 9 billion people

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Universal function-specificity of codon usage

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

ATTED-II provides coexpressed gene networks for Arabidopsis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Mapping and quantifying mammalian transcriptomes by RNA-Seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Sequence-based prediction of protein-protein interactions by means of codon usage.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

GeneCAT--novel webtools that combine BLAST and co-expression analyses.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Conserved co-expression for candidate disease gene prioritization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Tissue-specific codon usage and the expression of human genes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

Analyzing a portion of the ROC curve

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894708

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

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FPCP%2FPCT178

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FPCP%2FPCT178

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FPCP%2FPCT178

Synteny and Collinearity in Plant Genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FPCP%2FPCT178

Similarities of ordered gene lists.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FPCP%2FPCT178

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24334350

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/PCP/PCT178

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

24334350

1 reference