Evidence map›Paper›PMID 33264727›Full record

ArticleComputational biology and chemistry2021

Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker: An integrative-SNP ranking web-tool.

Younes Aftabi, Saleh Rafei, Habib Zarredar, Amir Amiri-Sadeghan, Mohsen Akbari-Shahpar, Zahra Khoshkam, Ensiyeh Seyedrezazadeh, Majid Khalili, Faramarz Mehrnejad, Sasan Fereidouni and 1 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computational biology and chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.2field-weighted citation impact, top 49% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Association ofIranian journal of basic medical sciences · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 6 institutions in 3 countries.

Younes AftabiTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran. Electronic address: aftabiy@tbzmed.ac.ir.
Saleh RafeiRazi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran.
Habib ZarredarTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
Amir Amiri-SadeghanTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
Mohsen Akbari-ShahparDepartment of Computer Engineering, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran.
Zahra KhoshkamTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran; Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Tehran, Tehran, Iran.
Ensiyeh SeyedrezazadehTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
Majid KhaliliTuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, P.O. Box: 53714161, Tabriz, Iran.
Faramarz MehrnejadDepartment of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.
Sasan FereidouniDepartment of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria.
B Paige LawrenceDepartments of Environmental Medicine and Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.
Tabriz University of Medical Sciences · IRRazi Vaccine and Serum Research Institute · IRUniversity of Rochester Medical Center · USUniversity of Tabriz · IRUniversity of Tehran · IRUniversity of Veterinary Medicine Vienna · AT

Funding

VISUAL INDICES OF NEUROTOXICITYP30ES001247 · NIEHS · UNIVERSITY OF ROCHESTER · PI Sally W Thurston · 1985 to 2026
$42.8M
NIEHS NIH HHS P30 ES001247
6 · The paper itself

Abstract

Different bioinformatic methods apply various approaches to predict how much the effect of a SNP could be deleterious and therefore their results may differ significantly. However, variation studies often need to consider an integrated prediction result to analyze the effect of SNPs. To address this problem, we used an algorithm to map ordinal predictions to a numeral space and averaging them, and based on it we developed the ISNPranker web-tool (http://isnpranker.semilab.ir/). It takes heterogonous outputs of different predictors and generates integrated numerical predictions and ranks SNPs based on them. Afterward, we used ISNPranker to identify the most deleterious coding SNPs (cSNPs) of the human aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that governs many molecular and cellular mechanisms and cSNPs may affect its structure, interactions, and function. Forty validated cSNPs of AHR were initially analyzed using 16 publicly available SNP analyzers and the results were introduced to the ISNPranker and integrated predictions were obtained. The cSNPs were ranked in 34 levels of danger and rs200257782 in the ARNT dimerization domain (ADD

Indexed as

AlgorithmsHumansPolymorphism, Single NucleotideProtein DomainsReceptors, Aryl HydrocarbonReceptors, Aryl HydrocarbonAryl hydrocarbon receptorBioinformaticsFunctionISNPrankerPolymorphismStructure

Identifiers

PMID33264727
PMCPMC8815319
OpenAlexW3099279729

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.