Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing (Q34824553)

4 August 2017

title

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing (English)

1 reference

4 August 2017

1 reference

Shaojun Xie

2

0 references

author name string

Xin Qi

1

1 reference

4 August 2017

Yuwei Liu

3

1 reference

4 August 2017

Fei Yi

4

1 reference

4 August 2017

Jingjuan Yu

5

1 reference

4 August 2017

language of work or name

1 reference

17 July 2013

1 reference

4 August 2017

number of pages

15

1 reference

inferred from page(s)

published in

Plant Molecular Biology

1 reference

4 August 2017

volume

83

1 reference

4 August 2017

issue

4-5

1 reference

4 August 2017

page(s)

459-473

1 reference

The true story of the HD-Zip family

4 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

The 5'-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Repeat associated small RNAs vary among parents and following hybridization in maize

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Reference genome sequence of the model plant Setaria

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Computational identification and functional predictions of long noncoding RNA in Zea mays

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Involvement of CDSP 32, a drought-induced thioredoxin, in the response to oxidative stress in potato plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Rfam 11.0: 10 years of RNA families

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Small RNAs, DNA methylation and transposable elements in wheat

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long non-coding RNAs and chromatin regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Hahb-4, a sunflower homeobox-leucine zipper gene, is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Widespread dynamic DNA methylation in response to biotic stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

lincRNAs act in the circuitry controlling pluripotency and differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

bZIP transcription factors in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.).

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

ABF2, an ABRE-binding bZIP factor, is an essential component of glucose signaling and its overexpression affects multiple stress tolerance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Widespread transcription at neuronal activity-regulated enhancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

miRBase: integrating microRNA annotation and deep-sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

The developmental dynamics of the maize leaf transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Role of transposable elements in heterochromatin and epigenetic control

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long non-coding RNAs: insights into functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Sequencing technologies - the next generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

An expression atlas of rice mRNAs and small RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long noncoding RNAs with enhancer-like function in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

The role of small RNAs in abiotic stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

BEDTools: a flexible suite of utilities for comparing genomic features

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Rational siRNA design for RNA interference

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Quality control and preprocessing of metagenomic datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Plant PP2C phosphatases: emerging functions in stress signaling

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Regulatory network of gene expression in the drought and cold stress responses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Transcription factors in plant defense and stress responses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Small RNAs as big players in plant abiotic stress responses and nutrient deprivation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Proline: a multifunctional amino acid

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Long noncoding RNA as modular scaffold of histone modification complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Activation and repression of transcription by auxin-response factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Senescence- and drought-related changes in peroxidase and superoxide dismutase isoforms in leaves of Ramonda serbica

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Time of day shapes Arabidopsis drought transcriptomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

An abiotic stress-responsive bZIP transcription factor from wild and cultivated tomatoes regulates stress-related genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

WEGO: a web tool for plotting GO annotations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Gramene database in 2010: updates and extensions

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Genome-wide transcriptome analysis of two maize inbred lines under drought stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11103-013-0104-6

PlantTFDB: a comprehensive plant transcription factor database

21 January 2018

1 reference

12 December 2020

Oxidative stress induced heat shock factor phosphorylation and HSF-dependent activation of yeast metallothionein gene transcription

1 reference

12 December 2020

The cell wall hydroxyproline-rich glycoprotein RSH is essential for normal embryo development in Arabidopsis

1 reference

12 December 2020

Plant productivity and environment

1 reference

12 December 2020

Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABA-responsive complexes each containing a G-box and a novel cis-acting element

1 reference

12 December 2020

The Maize Abscisic Acid-Responsive Protein Rab17 Is Located in the Nucleus and Interacts with Nuclear Localization Signals

1 reference

12 December 2020

Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways

1 reference

12 December 2020

Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses

1 reference

12 December 2020

A novel function for a redox-related LEA protein (SAG21/AtLEA5) in root development and biotic stress responses

1 reference

12 December 2020

The ARF family of transcription factors and their role in plant hormone-responsive transcription

1 reference

12 December 2020

The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana

1 reference

12 December 2020

Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola

1 reference

12 December 2020

Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

1 reference

12 December 2020

10.1007/S11103-013-0104-6

Identifiers

DOI

1 reference

4 August 2017

1 reference