Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice (Q34622310)

3 August 2017

Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice (English)

1 reference

3 August 2017

7

1 reference

3 August 2017

Yu-Chan Zhang

1

1 reference

3 August 2017

Jian-You Liao

2

1 reference

3 August 2017

Ze-Yuan Li

3

1 reference

3 August 2017

Yang Yu

4

1 reference

3 August 2017

Jin-Ping Zhang

5

1 reference

3 August 2017

Quan-Feng Li

6

1 reference

3 August 2017

Wen-Sheng Shu

8

1 reference

3 August 2017

Yue-Qin Chen

9

1 reference

3 August 2017

3 December 2014

1 reference

3 August 2017

1 reference

3 August 2017

15

1 reference

3 August 2017

12

1 reference

3 August 2017

512

1 reference

Creative Commons Attribution 4.0 International

3 August 2017

start time

1 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

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

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-014-0512-1

0 references

cites work

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Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice

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Long non-coding RNAs: new players in cell differentiation and development

7 July 2018

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Long noncoding RNAs: new regulators in plant development

7 July 2018

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Evolutionary conservation of microRNA regulatory programs in plant flower development

7 July 2018

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

7 July 2018

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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

7 July 2018

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The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

7 July 2018

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Long noncoding RNAs in C. elegans

7 July 2018

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

7 July 2018

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Modular regulatory principles of large non-coding RNAs

7 July 2018

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.

7 July 2018

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

7 July 2018

1 reference

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The Pfam protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Long noncoding RNAs with enhancer-like function in human cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Transcriptome-wide identification of microRNA targets in rice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

A new generation of homology search tools based on probabilistic inference

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Genome sequencing and analysis of the model grass Brachypodium distachyon

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The B73 Maize Genome: Complexity, Diversity, and Dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Origin, biogenesis, and activity of plant microRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The Sorghum bicolor genome and the diversification of grasses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Target mimicry provides a new mechanism for regulation of microRNA activity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The TIGR Rice Genome Annotation Resource: improvements and new features

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

RMD: a rice mutant database for functional analysis of the rice genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

OryGenesDB: a database for rice reverse genetics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Aligning multiple genomic sequences with the threaded blockset aligner

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Cytoscape: a software environment for integrated models of biomolecular interaction networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

CLICK and EXPANDER: a system for clustering and visualizing gene expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

AU-rich elements: characterization and importance in mRNA degradation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Parental imprinting of the mouse H19 gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253996

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

T-DNA insertional mutagenesis for functional genomics in rice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Differential expression of TPS11, a phosphate starvation-induced gene in tomato

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

RBE controls microRNA164 expression to effect floral organogenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

ceRNAs: miRNA target mimic mimics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

A highly efficient transient protoplast system for analyzing defence gene expression and protein-protein interactions in rice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0512-1

A long noncoding RNA activated by TGF-β promotes the invasion-metastasis cascade in hepatocellular carcinoma

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25517485

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-014-0512-1

1 reference

Dimensions Publication ID

3 August 2017

0 references

1 reference

3 August 2017

1 reference