A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. (Q52690560)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

title

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Hannah Carter

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

John Paul Shen

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Emma K Farley

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Jason F Kreisberg

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Trey Ideker

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

15

Michael Snyder

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

author name string

Ana Bojorquez-Gomez

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Daniel Ortiz Velez

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Guorong Xu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Kyle S Sanchez

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Kevin Chen

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Katherine Licon

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Collin Melton

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Katrina M Olson

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Michael Ku Yu

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Justin K Huang

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

Stephanie I Fraley

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

language of work or name

English

0 references

publication date

2 April 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

volume

50

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

page(s)

613-620

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/s41588-018-0091-2

22 March 2020

exact match

0 references

cites work

3D collagen architecture induces a conserved migratory and transcriptional response linked to vasculogenic mimicry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Activation of mutant TERT promoter by RAS-ERK signaling is a key step in malignant progression of BRAF-mutant human melanomas

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Challenges in identifying cancer genes by analysis of exome sequencing data.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A landscape of pharmacogenomic interactions in cancer.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Role of non-coding sequence variants in cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A gene-based association method for mapping traits using reference transcriptome data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Recurrent somatic mutations in regulatory regions of human cancer genomes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Integrative analysis of 111 reference human epigenomes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Integrated genomic characterization of papillary thyroid carcinoma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

TERT promoter mutations and gene amplification: promoting TERT expression in Merkel cell carcinoma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Genome-wide analysis of noncoding regulatory mutations in cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Three-dimensional cell migration does not follow a random walk

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

The Cancer Genome Atlas Pan-Cancer analysis project

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Network-based stratification of tumor mutations

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

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

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

25 August 2018

Cancer genome landscapes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Highly recurrent TERT promoter mutations in human melanoma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Chapter 11: Genome-wide association studies

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Integrative annotation of chromatin elements from ENCODE data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Streaming fragment assignment for real-time analysis of sequencing experiments

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

An integrated encyclopedia of DNA elements in the human genome

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Dvl2-dependent activation of Daam1 and RhoA regulates Wnt5a-induced breast cancer cell migration

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

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

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Fast gapped-read alignment with Bowtie 2

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A framework for variation discovery and genotyping using next-generation DNA sequencing data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Excessive activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide 2 (APOBEC2) contributes to liver and lung tumorigenesis.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Data-driven assessment of eQTL mapping methods

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

New approaches to population stratification in genome-wide association studies

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A human functional protein interaction network and its application to cancer data analysis

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A distinctive role for focal adhesion proteins in three-dimensional cell motility.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

International network of cancer genome projects

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

BEDTools: a flexible suite of utilities for comparing genomic features

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

EGFR signals to mTOR through PKC and independently of Akt in glioma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Mechanics, malignancy, and metastasis: the force journey of a tumor cell

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Increased copy number of the TERT and TERC telomerase subunit genes in cancer cells

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Mechanism of activation of the Formin protein Daam1

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Human small G proteins, ObgH1, and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

IL-2 increases human telomerase reverse transcriptase activity transcriptionally and posttranslationally through phosphatidylinositol 3'-kinase/Akt, heat shock protein 90, and mammalian target of rapamycin in transformed NK cells

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

IFN-gamma/IRF-1-induced p27kip1 down-regulates telomerase activity and human telomerase reverse transcriptase expression in human cervical cancer.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Hypoxia-inducible factor 1 mediates upregulation of telomerase (hTERT).

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A census of human cancer genes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Identification of novel Smad binding proteins

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

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

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Statistical significance for genomewide studies

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Wnt/Frizzled activation of Rho regulates vertebrate gastrulation and requires a novel Formin homology protein Daam1

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A CDK-independent function of mammalian Cks1: targeting of SCF(Skp2) to the CDK inhibitor p27Kip1.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

The p14ARF tumor suppressor protein facilitates nucleolar sequestration of hypoxia-inducible factor-1alpha (HIF-1alpha ) and inhibits HIF-1-mediated transcription

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Biochemical evidence that Escherichia coli hyi (orf b0508, gip) gene encodes hydroxypyruvate isomerase.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

Frizzled regulation of Notch signalling polarizes cell fate in the Drosophila eye.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5893414

A tutorial on spectral clustering

25 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41588-018-0091-2

inferred from DOI database lookup

7 January 2021

based on heuristic

Cox's Regression Model for Counting Processes: A Large Sample Study

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41588-018-0091-2

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/S41588-018-0091-2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29610481%20AND%20SRC:MED&resulttype=core&format=json

22 March 2020

1 reference