Evidence map›Paper›PMID 24710071›Full record

ArticlePloS one2014

S-score: a scoring system for the identification and prioritization of predicted cancer genes.

Jorge E S de Souza, André F Fonseca, Renan Valieris, Dirce M Carraro, Jean Y J Wang, Richard D Kolodner, Sandro J de Souza

Abstract read
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
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

6 citing papers in PubMed.

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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

7 authors.

Jorge E S de SouzaInstitute of Bioinformatics and Biotechnology, São Paulo, Brazil; Center for Cell Therapy and Regional Blood Center, Department of Clinical Medicine, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil; International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
André F FonsecaInstitute of Bioinformatics and Biotechnology, São Paulo, Brazil; Brain Institute, UFRN, Natal, Brazil.
Renan ValierisInstitute of Bioinformatics and Biotechnology, São Paulo, Brazil; International Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
Dirce M CarraroInternational Research Center, CIPE/AC Camargo Cancer Center, São Paulo, Brazil.
Jean Y J WangMoores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America.
Richard D KolodnerMoores-UCSD Cancer Center and Department of Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America; Ludwig Institute for Cancer Research, San Diego Branch, Department of Medicine and Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute of Genomic Medicine, University of California San Diego School of Medicine, San Diego, California, United States of America.
Sandro J de SouzaBrain Institute, UFRN, Natal, Brazil.

Funding

ENZYMATIC MECHANISMS OF GENETIC RECOMBINATIONR01GM026017 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Richard D Kolodner · 1985 to 2026
$10.5M
STRUCTURE AND FUNCTION OF THE C-ABL PROTO-ONCOPROTEINR01CA043054 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WANG, JEAN Y.J. · 1986 to 2018
$4.4M
ENZYMATIC MECHANISMS OF GENETIC RECOMBINATIONR37GM026017 · NIGMS · UNIVERSITY OF CALIFORNIA SAN DIEGO · PI KOLODNER, RICHARD D · 1992 to 2001
$759k
NCI NIH HHS R01 CA043054NIGMS NIH HHS GM26017NIGMS NIH HHS R01 GM026017NIGMS NIH HHS R37 GM026017
6 · The paper itself

Abstract

A new method, which allows for the identification and prioritization of predicted cancer genes for future analysis, is presented. This method generates a gene-specific score called the "S-Score" by incorporating data from different types of analysis including mutation screening, methylation status, copy-number variation and expression profiling. The method was applied to the data from The Cancer Genome Atlas and allowed the identification of known and potentially new oncogenes and tumor suppressors associated with different clinical features including shortest term of survival in ovarian cancer patients and hormonal subtypes in breast cancer patients. Furthermore, for the first time a genome-wide search for genes that behave as oncogenes and tumor suppressors in different tumor types was performed. We envisage that the S-score can be used as a standard method for the identification and prioritization of cancer genes for follow-up studies.

Indexed as

Computational BiologyDNA Copy Number VariationsFemaleGene Expression Regulation, NeoplasticGenes, NeoplasmGenomicsHumansMethylationMutationNeoplasmsOncogenes

Identifiers

PMID24710071
PMCPMC3978018

What OpenQuestion holds

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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.