Evidence map›Paper›PMID 24348198›Full record

ArticleTheScientificWorldJournal2013

Feature-based classification of amino acid substitutions outside conserved functional protein domains.

Branislava Gemovic, Vladimir Perovic, Sanja Glisic, Nevena Veljkovic

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

Article in TheScientificWorldJournal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.5field-weighted citation impact, top 27% 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

4 citing papers in PubMed, 9 citations in OpenAlex.

  1. Article
  2. Review
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  4. 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

4 authors at 1 institution in 1 country.

Branislava GemovicCentre for Multidisciplinary Research and Engineering, Vinca Institute of Nuclear Sciences, University of Belgrade, 12-14 Mihajla Petrovica Alasa, 11001 Belgrade, Serbia.
Vladimir PerovicCentre for Multidisciplinary Research and Engineering, Vinca Institute of Nuclear Sciences, University of Belgrade, 12-14 Mihajla Petrovica Alasa, 11001 Belgrade, Serbia.
Sanja GlisicCentre for Multidisciplinary Research and Engineering, Vinca Institute of Nuclear Sciences, University of Belgrade, 12-14 Mihajla Petrovica Alasa, 11001 Belgrade, Serbia.
Nevena VeljkovicCentre for Multidisciplinary Research and Engineering, Vinca Institute of Nuclear Sciences, University of Belgrade, 12-14 Mihajla Petrovica Alasa, 11001 Belgrade, Serbia.
University of Belgrade · RS

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Indexed as

Amino Acid SubstitutionAlgorithmsComputational BiologyDatabases, GeneticDioxygenasesDNA-Binding ProteinsDNA (Cytosine-5-)-MethyltransferasesDNA Methyltransferase 3AEnhancer of Zeste Homolog 2 ProteinEpigenesis, GeneticHumansPolycomb Repressive Complex 2Protein Interaction Domains and MotifsProteinsProto-Oncogene ProteinsRepressor ProteinsASXL1 protein, humanDioxygenasesDNA-Binding ProteinsDNA (Cytosine-5-)-MethyltransferasesDNA Methyltransferase 3ADNMT3A protein, humanEnhancer of Zeste Homolog 2 ProteinEZH2 protein, humanPolycomb Repressive Complex 2ProteinsProto-Oncogene ProteinsRepressor ProteinsTET2 protein, human

Identifiers

PMID24348198
PMCPMC3855963
OpenAlexW2155988965

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.