Bioinformatics analyses of retinoblastoma reveal the retinoblastoma progression subtypes

PeerJ
Manjing CaoWanpeng Wang

Abstract

Retinoblastoma (RB) is one common pediatric malignant tumor with dismal outcomes. Heterogeneity of RB and subtypes of RB were identified but the association between the subtypes of RB and RB progression have not been fully investigated. Four public datasets were downloaded from Gene expression omnibus and normalization was performed to remove batch effect. Two public datasets were explored to obtain the RB progression gene signatures by differentially expression analysis while another two datasets were iterated for RB subtypes identification using consensus clustering. After the RB progressive subtype gene signatures were identified, we tested the diagnostic capacity of these gene signatures by receiver operation curve. Three hundreds and forty six genes that were enriched in cell cycle were identified as the progression signature in RB from two independent datasets. Four subtypes of RB were stratified by consensus clustering. A total of 21 genes from RB progression signature were differentially expressed between RB subtypes. One subtype with low expression cell division genes have less progression of all four subtypes. A panel of five RB subtype genes (CLUL1, CNGB1, ROM1, LRRC39 and RDH12) predict progression of RB. Retinoblas...Continue Reading

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Citations

Mar 9, 2021·Computational and Mathematical Methods in Medicine·Min ZhangCui Ma

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Datasets Mentioned

BETA
GSE110811
GSE59983
GSE97508

Methods Mentioned

BETA
PCR
PCA
single cell sequencing

Software Mentioned

Bioconductor
ConsensusClusterPlus
limma
limma Bioconductor
Metascape
SigClust
clusterProfiler
GEOquery

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