Evidence map›Paper›PMID 32209064›Full record

ArticleBMC ophthalmology2020

Integrated bioinformatics analysis of aberrantly-methylated differentially-expressed genes and pathways in age-related macular degeneration.

Yinchen Shen, Mo Li, Kun Liu, Xiaoyin Xu, Shaopin Zhu, Ning Wang, Wenke Guo, Qianqian Zhao, Ping Lu, Fudong Yu and 1 more

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

Article in BMC ophthalmology, 2020. 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
0.8field-weighted citation impact, top 29% 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

6 citing papers in PubMed, 10 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

11 authors at 5 institutions in 1 country.

Yinchen ShenDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China.
Mo LiBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
Kun LiuDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China.
Xiaoyin XuDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China.
Shaopin ZhuDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China.
Ning WangDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China.
Wenke GuoNHC Key Lab. of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, China.
Qianqian ZhaoNHC Key Lab. of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, China.
Ping LuNHC Key Lab. of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, China.
Fudong YuNHC Key Lab. of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai, China.
Xun XuDepartment of Ophthalmology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200080, People's Republic of China. drxuxun@sjtu.edu.cn.
Shanghai First People's Hospital · CNShanghai Institute of Planned Parenthood Research · CNShanghai Eye Disease Prevention & Treatment Center · CNFudan University · CNShanghai Jiao Tong University · CN

Funding

National Key R&D Program of China 2016YFC0904800, 2019YFC0840607National Natural Science Foundation of China 81800831, 81800799National Science and Technology Major Project of China 2017ZX09304010Shanghai Municipal Commission of Health and Family Planning 201740088
6 · The paper itself

Abstract

backgroundAge-related macular degeneration (AMD) represents the leading cause of visual impairment in the aging population. The goal of this study was to identify aberrantly-methylated, differentially-expressed genes (MDEGs) in AMD and explore the involved pathways via integrated bioinformatics analysis.

methodsData from expression profile GSE29801 and methylation profile GSE102952 were obtained from the Gene Expression Omnibus database. We analyzed differentially-methylated genes and differentially-expressed genes using R software. Functional enrichment and protein-protein interaction (PPI) network analysis were performed using the R package and Search Tool for the Retrieval of Interacting Genes online database. Hub genes were identified using Cytoscape.

resultsIn total, 827 and 592 genes showed high and low expression, respectively, in GSE29801; 4117 hyper-methylated genes and 511 hypo-methylated genes were detected in GSE102952. Based on overlap, we categorized 153 genes as hyper-methylated, low-expression genes (Hyper-LGs) and 24 genes as hypo-methylated, high-expression genes (Hypo-HGs). Four Hyper-LGs (CKB, PPP3CA, TGFB2, SOCS2) overlapped with AMD risk genes in the Public Health Genomics and Precision Health Knowledge Base. KEGG pathway enrichment analysis indicated that Hypo-HGs were enriched in the calcium signaling pathway, whereas Hyper-LGs were enriched in sphingolipid metabolism. In GO analysis, Hypo-HGs were enriched in fibroblast migration, membrane raft, and coenzyme binding, among others. Hyper-LGs were enriched in mRNA transport, nuclear speck, and DNA binding, among others. In PPI network analysis, 23 nodes and two edges were established from Hypo-HGs, and 151 nodes and 73 edges were established from Hyper-LGs. Hub genes (DHX9, MAPT, PAX6) showed the greatest overlap.

conclusionThis study revealed potentially aberrantly MDEGs and pathways in AMD, which might improve the understanding of this disease.

Indexed as

Gene Expression ProfilingComputational BiologyDEAD-box RNA HelicasesDNA MethylationGene Regulatory NetworksGenetic MarkersHumansMacular DegenerationNeoplasm ProteinsPAX6 Transcription FactorProtein Interaction Mapstau ProteinsDEAD-box RNA HelicasesDHX9 protein, humanGenetic MarkersMAPT protein, humanNeoplasm ProteinsPAX6 protein, humanPAX6 Transcription Factortau ProteinsAge-related macular degenerationBioinformatics analysisChoroidal neovascularizationGene expressionMethylation

Identifiers

PMID32209064
PMCPMC7092446
OpenAlexW3013614404

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.