Evidence map›Paper›PMID 26635391›Full record

ArticleNucleic acids research2016

DriverDBv2: a database for human cancer driver gene research.

I-Fang Chung, Chen-Yang Chen, Shih-Chieh Su, Chia-Yang Li, Kou-Juey Wu, Hsei-Wei Wang, Wei-Chung Cheng

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
65citing papers in PubMed, 1 pooled it
–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

65 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  6. Memory-promoting function of miR-379-5p attenuates CD8Journal for immunotherapy of cancer · 2025
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  20. miR-4759 suppresses breast cancer through immune checkpoint blockade.Computational and structural biotechnology journal · 2022
    Article

5 more citing papers are in PubMed but not listed here.

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.

I-Fang ChungInstitute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, 11221, Taiwan.
Chen-Yang ChenInstitute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
Shih-Chieh SuResearch Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan.
Chia-Yang LiDepartment of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
Kou-Juey WuResearch Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan Graduate Institute of Cancer Biology, China Medical University, Taichung, 40402, Taiwan.
Hsei-Wei WangVGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 11221, Taiwan Department of Education and Research, Taipei City Hospital, Taipei 10341, Taiwan hwwang@ym.edu.tw.
Wei-Chung ChengResearch Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan Graduate Institute of Cancer Biology, China Medical University, Taichung, 40402, Taiwan cwc0702@gmail.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We previously presented DriverDB, a database that incorporates ∼ 6000 cases of exome-seq data, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. The database provides two points of view, 'Cancer' and 'Gene', to help researchers visualize the relationships between cancers and driver genes/mutations. In the updated DriverDBv2 database (http://ngs.ym.edu.tw/driverdb) presented herein, we incorporated >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and published papers. Seven additional computational algorithms (meaning that the updated database contains 15 in total), which were developed for driver gene identification, are incorporated into our analysis pipeline, and the results are provided in the 'Cancer' section. Furthermore, there are two main new features, 'Expression' and 'Hotspot', in the 'Gene' section. 'Expression' displays two expression profiles of a gene in terms of sample types and mutation types, respectively. 'Hotspot' indicates the hotspot mutation regions of a gene according to the results provided by four bioinformatics tools. A new function, 'Gene Set', allows users to investigate the relationships among mutations, expression levels and clinical data for a set of genes, a specific dataset and clinical features.

Indexed as

Databases, GeneticGenes, NeoplasmMutationGene Expression ProfilingHumansNeoplasmsSequence Analysis

Identifiers

PMID26635391
PMCPMC4702919

What Socratic holds

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LicenceCC BY-NC
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 Socratic graph.