Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events (Q42374923)

28 October 2017

Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events (English)

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28 October 2017

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2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28959951 AND SRC:MED&resulttype=core&format=json

1 June 2020

Simranjit X Singh

4

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1 June 2020

author name string

Arghavan Ashouri

1

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1 June 2020

Jimmy Van den Eynden

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28959951 AND SRC:MED&resulttype=core&format=json

1 June 2020

Thales Papagiannakopoulos

5

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28959951 AND SRC:MED&resulttype=core&format=json

1 June 2020

Erik Larsson

6

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1 June 2020

language of work or name

English

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publication date

25 October 2016

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28 October 2017

Nature Communications

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1 June 2020

volume

7

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1 June 2020

page(s)

13197

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Creative Commons Attribution 4.0 International

1 June 2020

copyright license

start time

25 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

The Dual Roles of NRF2 in Cancer.

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Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth

28 May 2018

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TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer

28 May 2018

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p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses

28 May 2018

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MYC-repressed long noncoding RNAs antagonize MYC-induced cell proliferation and cell cycle progression

28 May 2018

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SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

28 May 2018

1 reference

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Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

28 May 2018

1 reference

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Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA.

28 May 2018

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HISAT: a fast spliced aligner with low memory requirements

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The landscape of long noncoding RNAs in the human transcriptome

28 May 2018

1 reference

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MYC regulates the non-coding transcriptome.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

NKD1 marks intestinal and liver tumors linked to aberrant Wnt signaling.

28 May 2018

1 reference

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HTSeq--a Python framework to work with high-throughput sequencing data

28 May 2018

1 reference

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NRF2/long noncoding RNA ROR signaling regulates mammary stem cell expansion and protects against estrogen genotoxicity

28 May 2018

1 reference

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A549 cell proliferation inhibited by RNAi mediated silencing of the Nrf2 gene

28 May 2018

1 reference

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Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Brevican knockdown reduces late-stage glioma tumor aggressiveness.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Antioxidants accelerate lung cancer progression in mice

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Sequencing depth and coverage: key considerations in genomic analyses

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The emerging role of the Nrf2-Keap1 signaling pathway in cancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Mutational heterogeneity in cancer and the search for new cancer-associated genes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Characterization of a novel long noncoding RNA, SCAL1, induced by cigarette smoke and elevated in lung cancer cell lines

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

X chromosome inactivation and epigenetic responses to cellular reprogramming

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

28 May 2018

p53 mutations in cancer

1 reference

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Troy, a tumor necrosis factor receptor family member, interacts with lgr5 to inhibit wnt signaling in intestinal stem cells.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Comprehensive molecular portraits of human breast tumours

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

GENCODE: the reference human genome annotation for The ENCODE Project

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Landscape of transcription in human cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

LincRNA-p21 suppresses target mRNA translation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The emergence of lncRNAs in cancer biology

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Non-coding RNAs in human disease

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Genomewide characterization of non-polyadenylated RNAs

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Differential expression analysis for sequence count data

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Supervised risk predictor of breast cancer based on intrinsic subtypes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

RNAi-mediated silencing of nuclear factor erythroid-2-related factor 2 gene expression in non-small cell lung cancer inhibits tumor growth and increases efficacy of chemotherapy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Identification of polymorphic antioxidant response elements in the human genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Transcriptional profiling identifies cyclin D1 as a critical downstream effector of mutant epidermal growth factor receptor signaling

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Dysfunctional KEAP1-NRF2 interaction in non-small-cell lung cancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

The transcriptional landscape of the mammalian genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Stress-specific signatures: expression profiling of p53 wild-type and -null human cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

A census of human cancer genes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Gene profiling of a myeloma cell line reveals similarities and unique signatures among IL-6 response, N-ras-activating mutations, and coculture with bone marrow stromal cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Role of histone H3 lysine 27 methylation in X inactivation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Isolation of NF-E2-related factor 2 (Nrf2), a NF-E2-like basic leucine zipper transcriptional activator that binds to the tandem NF-E2/AP1 repeat of the beta-globin locus control region

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

YY1 binds to α-synuclein 3'-flanking region SNP and stimulates antisense noncoding RNA expression.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Nrf2 redirects glucose and glutamine into anabolic pathways in metabolic reprogramming.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5093340

Loss of one copy of Zfp148 reduces lesional macrophage proliferation and atherosclerosis in mice by activating p53

16 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038/NCOMMS13197

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NCOMMS13197

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28959951 AND SRC:MED&resulttype=core&format=json

1 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28959951 AND SRC:MED&resulttype=core&format=json

1 June 2020

PubMed publication ID

28959951

1 reference