Evidence map›Paper›PMID 37179305›Full record

ArticleBMC medical genomics2023

Retinoblastoma gene expression profiling based on bioinformatics analysis.

Jun Mao, Mingzhi Lu, Siduo Lu, Yiqiao Xing, Xuejiao Xu, Ying Chen, Huirong Xu, Wei Zuo, Jingwen Zhou, Wei Du

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

Article in BMC medical genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 35% 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

3 citing papers in PubMed, 2 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
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

10 authors at 3 institutions in 1 country.

Jun Mao *The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Mingzhi Lu *Aier Eye Hospital of Wuhan University, Wuhan, China.
Siduo Lu *The First Affiliated Hospital of Kunming Medical University, Yunnan, China.
Yiqiao XingAier Eye Hospital of Wuhan University, Wuhan, China.
Xuejiao XuThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Ying ChenThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Huirong XuThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Wei ZuoThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Jingwen ZhouThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China.
Wei DuThe Eighth Affiliated Hospital of Sun Yat-sen University, Shenzheng, China. foxfeiniao@163.com.
Sun Yat-sen University · CNWuhan University · CNKunming Medical University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundRetinoblastoma (RB) is frequently occurring malignant tumors that originate in the retina, and their exact cause and development mechanisms are yet to be fully comprehended. In this study, we identified possible biomarkers for RB and delved into the molecular mechanics linked with such markers.

methodsIn this study GSE110811 and GSE24673 were analyzed. Weighted gene co-expression network analysis (WGCNA) was applied to screen modules and genes associated with RB. By overlapping RB-related module genes with differentially expressed genes (DEGs) between RB and control samples, differentially expressed retinoblastoma genes (DERBGs) were acquired. A gene ontology (GO) enrichment analysis and a kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were conducted to explore the functions of these DERBGs. To study the protein interactions of DERBGs, a protein-protein interaction (PPI) network was constructed. Hub DERBGs were screened using the least absolute shrinkage and selection operator (LASSO) regression analysis, as well as the random forest (RF) algorithm. Additionally, the diagnostic performance of RF and LASSO methods was evaluated using receiver operating characteristic (ROC) curves and single-gene gene set enrichment analysis (GSEA) was conducted to explore the potential molecular mechanisms involved with these Hub DERBGs. In addition, the competing endogenous RNA (ceRNA) regulatory network of Hub DERBGs was constructed.

resultAbout 133 DERBGs were found to be associated with RB. GO and KEGG enrichment analyses revealed that the important pathways of these DERBGs. Furthermore, the PPI network revealed 82 DERBGs interacting with each other. By RF and LASSO methods, PDE8B, ESRRB, and SPRY2 were identified as Hub DERBGs in patients with RB. From the expression assessment of Hub DERBGs, it was found that the levels of expression of PDE8B, ESRRB, and SPRY2 were significantly decreased in the tissues of RB tumors. Secondly, single-gene GSEA revealed a connection between these 3 Hub DERBGs and oocyte meiosis, cell cycle, and spliceosome. Finally, the ceRNA regulatory network revealed that hsa-miR-342-3p, hsa-miR-146b-5p, hsa-miR-665, and hsa-miR-188-5p may play a central role in the disease.

conclusionHub DERBGs may provide new insight into RB diagnosis and treatment based on the understanding of disease pathogenesis.

Indexed as

MicroRNAsRetinal NeoplasmsRetinoblastomaComputational BiologyGene Expression ProfilingGene Regulatory NetworksHumansIntracellular Signaling Peptides and ProteinsMembrane ProteinsRetinaIntracellular Signaling Peptides and ProteinsMembrane ProteinsMicroRNAsMIRN188 microRNA, humanMIRN665 microRNA, humanSPRY2 protein, humanBioinformatics analysisBiomarkersceRNARegulatory networkRetinoblastoma

Identifiers

PMID37179305
PMCPMC10183129
OpenAlexW4376642785

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.