GLAD4U: deriving and prioritizing gene lists from PubMed literature (Q34530676)

2 August 2017

title

GLAD4U: deriving and prioritizing gene lists from PubMed literature (English)

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2 August 2017

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Jérôme Jourquin

1

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2 August 2017

Dexter Duncan

series ordinal

2

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2 August 2017

Zhiao Shi

series ordinal

3

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2 August 2017

Bing Zhang

series ordinal

4

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2 August 2017

language of work or name

English

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publication date

17 December 2012

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2 August 2017

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2 August 2017

volume

13 Suppl 8

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2 August 2017

page(s)

S20

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describes a project that uses

2 August 2017

Cytoscape

object named as

Cytoscape

cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Cytoscape

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cites work

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Genetic variants of connexin37 are associated with carotid intima-medial thickness and future onset of ischemic stroke

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Overexpression of SCYL1‐BP1 stabilizes functional p53 by suppressing MDM2‐mediated ubiquitination

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Counteracting MDM2-induced HIPK2 downregulation restores HIPK2/p53 apoptotic signaling in cancer 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=3535723

A High-Frequency Regulatory Polymorphism in the p53 Pathway Accelerates Tumor 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=3535723

HDMX-L is expressed from a functional p53-responsive promoter in the first intron of the HDMX gene and participates in an autoregulatory feedback loop to control p53 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=3535723

S6K1 is a multifaceted regulator of Mdm2 that connects nutrient status and DNA damage response

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Pharmacogenetic association of hypertension candidate genes with fasting glucose in the GenHAT Study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Maternal angiotensinogen (AGT) haplotypes, fetal renin (REN) haplotypes and risk of preeclampsia; estimation of gene-gene interaction from family-triad 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=3535723

Association of plasma retinol-binding protein 4, adiponectin, and high molecular weight adiponectin with insulin resistance in non-diabetic hypertensive patients

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Mechanisms linking obesity, chronic kidney disease, and fatty liver disease: the roles of fetuin-A, adiponectin, and AMPK.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Genetic variation in CYP27B1 is associated with congestive heart failure in patients with hypertension

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Human inhibitor of growth 1 inhibits hepatoma cell growth and influences p53 stability in a variant-dependent manner

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Tethering by lamin A stabilizes and targets the ING1 tumour suppressor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Interspecies data mining to predict novel ING-protein interactions in human

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

FACTA: a text search engine for finding associated biomedical concepts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

ING1a expression increases during replicative senescence and induces a senescent phenotype

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

ING1 protein targeting to the nucleus by karyopherins is necessary for activation of p21.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Histone H3K4me3 Binding Is Required for the DNA Repair and Apoptotic Activities of ING1 Tumor Suppressor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

NAD(P)H quinone oxidoreductase 1 inhibits the proteasomal degradation of the tumour suppressor p33(ING1b)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Walking the interactome for prioritization of candidate disease 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=3535723

Improved human disease candidate gene prioritization using mouse phenotype

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Phosphorylation of the tumor suppressor p33(ING1b) at Ser-126 influences its protein stability and proliferation of melanoma 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=3535723

The ING1b tumor suppressor facilitates nucleotide excision repair by promoting chromatin accessibility to XPA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

EBIMed--text crunching to gather facts for proteins from Medline

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate 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=3535723

Gene prioritization through genomic data fusion

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

A functional link between the tumour suppressors ARF and p33ING1.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Status of text-mining techniques applied to biomedical text

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Literature mining for the biologist: from information retrieval to biological discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

WebGestalt: an integrated system for exploring gene sets in various biological contexts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Integration of text- and data-mining using ontologies successfully selects disease gene candidates

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Textpresso: an ontology-based information retrieval and extraction system for biological literature

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

The genetic association 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=3535723

GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

PubMatrix: a tool for multiplex literature mining

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

POCUS: mining genomic sequence annotation to predict disease 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=3535723

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Association of genes to genetically inherited diseases using data mining

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Mining the bibliome: searching for a needle in a haystack? New computing tools are needed to effectively scan the growing amount of scientific literature for useful information

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

A literature network of human genes for high-throughput analysis of gene 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=3535723

Gene ontology: tool for the unification of 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=3535723

MDM2 as a modifier gene in retinoblastoma

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Cellular expression of renal, cardiac and pulmonary inducible nitric oxide synthase in double-transgenic mice expressing human renin and angiotensinogen genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Resveratrol induces mitochondrial biogenesis and ameliorates Ang II-induced cardiac remodeling in transgenic rats harboring human renin and angiotensinogen genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Hypoadiponectinemia is associated with prehypertension in obese individuals of multiethnic origin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Adiponectin - A possible factor in the pathogenesis of carbohydrate metabolism disturbances in patients with pheochromocytoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Low plasma adiponectin concentration is associated with myocardial infarction in young individuals

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Association of the renin gene polymorphism, three angiotensinogen gene polymorphisms and the haplotypes with essential hypertension in the Mongolian population

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Renin-angiotensin-aldosterone system gene polymorphisms in coronary artery bypass graft surgery patients.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

AliBaba: PubMed as a graph

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Are cell cycle and apoptosis genes associated with prostate cancer risk in North Indian population?

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Linking microarray data to the literature.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Confirmation That the Renin Gene Distal Enhancer Polymorphism REN -5312C/T Is Associated With Increased Blood Pressure

27 October 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Association of genetic variants in the adiponectin gene with adiponectin level and hypertension in Hong Kong Chinese

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-13-S8-S20

Plasma adiponectin levels are associated with left ventricular hypertrophy in a random sample of middle-aged subjects

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3535723

Association of renin BglI polymphism with essential hypertension: a meta-analysis involving 1811 cases and 1626 controls

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23282288

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-S8-S20

1 reference

Dimensions Publication ID

2 August 2017

0 references

1 reference

2 August 2017

1 reference