Evidence map›Paper›PMID 33823876›Full record

ArticleBMC medical genomics2021

Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis.

Guoliang Jia, Zheyu Song, Zhonghang Xu, Youmao Tao, Yuanyu Wu, Xiaoyu Wan

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

Article in BMC medical genomics, 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
0.5field-weighted citation impact, top 39% 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, 11 citations in OpenAlex.

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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

6 authors at 2 institutions in 1 country.

Guoliang JiaDepartment of Orthopedics, The Second Clinical Hospital of Jilin University, NO.218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin, China.
Zheyu SongDepartment of Gastrointestinal and Colorectal Surgery, The Third Hospital of Jilin University, No.126, Xiantai Street, Changchun, 130033, Jilin, China.
Zhonghang XuDepartment of Gastrointestinal and Colorectal Surgery, The Third Hospital of Jilin University, No.126, Xiantai Street, Changchun, 130033, Jilin, China.
Youmao TaoDepartment of Gastrointestinal and Colorectal Surgery, The Third Hospital of Jilin University, No.126, Xiantai Street, Changchun, 130033, Jilin, China.
Yuanyu WuDepartment of Gastrointestinal and Colorectal Surgery, The Third Hospital of Jilin University, No.126, Xiantai Street, Changchun, 130033, Jilin, China. wyy511@jlu.edu.cn.ORCID 0000-0002-2252-4011
Xiaoyu WanDepartment of Brest Surgery, The Second Clinical Hospital of Jilin University, NO.218, Ziqiang Street, Nanguan District, Changchun, 130000, Jilin, China. wanxy17@mails.jlu.edu.cn.
Jilin University · CNSecond Affiliated Hospital of Jilin University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundBioinformatics was used to analyze the skin cutaneous melanoma (SKCM) gene expression profile to provide a theoretical basis for further studying the mechanism underlying metastatic SKCM and the clinical prognosis.

methodsWe downloaded the gene expression profiles of 358 metastatic and 102 primary (nonmetastatic) CM samples from The Cancer Genome Atlas (TCGA) database as a training dataset and the GSE65904 dataset from the National Center for Biotechnology Information database as a validation dataset. Differentially expressed genes (DEGs) were screened using the limma package of R3.4.1, and prognosis-related feature DEGs were screened using Logit regression (LR) and survival analyses. We also used the STRING online database, Cytoscape software, and Database for Annotation, Visualization and Integrated Discovery software for protein-protein interaction network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses based on the screened DEGs.

resultsOf the 876 DEGs selected, 11 (ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C) were screened using LR analysis. The survival prognosis of nonmetastatic group was better compared to the metastatic group between the TCGA training and validation datasets. The 11 DEGs were involved in 9 KEGG signaling pathways, and of these 11 DEGs, CALML5 was a feature DEG involved in the melanogenesis pathway, 12 targets of which were collected.

conclusionThe feature DEGs screened, such as CALML5, are related to the prognosis of metastatic CM according to LR. Our results provide new ideas for exploring the molecular mechanism underlying CM metastasis and finding new diagnostic prognostic markers.

Indexed as

Biomarkers, TumorCutaneous Malignant MelanomaMelanomaSkin NeoplasmsComputational BiologyGene Expression ProfilingGene Expression Regulation, NeoplasticGenetic MarkersHumansLogistic ModelsNeoplasm MetastasisPrognosisProtein Interaction MapsSurvival AnalysisBiomarkers, TumorGenetic MarkersBioinformaticsCutaneous melanomaDifferentially expressed genesMetastasisPrognosis

Identifiers

PMID33823876
PMCPMC8022370
OpenAlexW3152253825

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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.