Evidence map›Paper›PMID 29617661›Full record

ArticleCell reports2018

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.

Zhongqi Ge, Jake S Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang and 7 more

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

Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.

0numbers the graph read from it
0cells of the map it votes in
80citing papers in PubMed
6.8field-weighted citation impact, top 2% 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

80 citing papers in PubMed, 123 citations in OpenAlex.

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20 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

17 authors at 4 institutions in 1 country.

Zhongqi GeDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jake S LeightonDepartment of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Yumeng WangDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
Xinxin PengDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Zhongyuan ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77005, USA.
Hu ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
Yutong SunDepartment of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Fan YaoDepartment of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jun LiDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Huiwen ZhangDepartment of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
Jianfang LiuChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA.
Craig D ShriverMurtha Cancer Center, Uniformed Services University/Walter Reed National Military Medical Center, Bethesda, MD 20889, USA.
Hai HuChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA.
Cancer Genome Atlas Research Network
Helen Piwnica-WormsDepartment of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Li MaDepartment of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Han LiangDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: hliang1@mdanderson.org.
The University of Texas MD Anderson Cancer Center · USWindber Research Institute · USThe University of Texas Health Science Center at Houston · USWalter Reed National Military Medical Center · US

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
Gene Expression Patterns in Human Tumors Identified Using Transcript SequencingU24CA143848 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, PEROU, CHARLES M · 2009 to 2016
$20.8M
Genome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0M
The Cancer Genome Atlas Data Analysis CenterU24CA143845 · NCI · BROAD INSTITUTE, INC. · PI CHIN, LYNDA, GETZ, GAD A · 2009 to 2016
$16.0M
Harvard Genome Characterization CenterU24CA144025 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHERLAPATI, RAJU S. · 2009 to 2016
$14.0M
The USC-JHU Cancer Epigenome Characterization CenterU24CA143882 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BAYLIN, STEPHEN B., WEISENBERGER, DANIEL JOSEPH · 2009 to 2016
$13.3M
MSKCC Center for Translational Cancer Genomic AnalysisU24CA143840 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI LADANYI, MARC, SANDER, CHRIS · 2009 to 2016
$11.5M
Cancer transcriptome characterization using massively parallel DNA sequencingU24CA143866 · NCI · BRITISH COLUMBIA CANCER AGENCY · PI MARRA, MARCO ANTONIO · 2009 to 2015
$10.9M
Integrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC)U24CA143883 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI AKBANI, REHAN, MILLS, GORDON B. · 2009 to 2016
$10.6M
NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA163722NCI NIH HHS R01 CA166051NCI NIH HHS R01 CA175486NCI NIH HHS R01 CA181029NCI NIH HHS R50 CA221675NCI NIH HHS U24 CA143799NCI NIH HHS U24 CA143835NCI NIH HHS U24 CA143840NCI NIH HHS U24 CA143843NCI NIH HHS U24 CA143845NCI NIH HHS U24 CA143848NCI NIH HHS U24 CA143858NCI NIH HHS U24 CA143866NCI NIH HHS U24 CA143867NCI NIH HHS U24 CA143882NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA144025NCI NIH HHS U24 CA209851NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210950NCI NIH HHS U24 CA210957NCI NIH HHS U24 CA210990NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG003273
6 · The paper itself

Abstract

Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies.

Indexed as

Gene Expression Regulation, NeoplasticUbiquitinationCell Line, TumorGenome, HumanGenomicsHumansMetabolic Networks and PathwaysNeoplasmsOncogene ProteinsOncogene Proteinsbiomarkercancer prognosisFBXW7pan-cancer analysisThe Cancer Genome Atlastherapeutic targetstumor subtypeubiquitin pathway

Identifiers

PMID29617661
PMCPMC5916807
OpenAlexW2796464520

What OpenQuestion holds

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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.