Fig. 1: Weighted gene co-expression network analysis (WGCNA) and m-fuzz clustering analysis reveals the overall and stage-specific lncRNA biotypes during cortical neuronal differentiation. | Cell Death Discovery

Fig. 1: Weighted gene co-expression network analysis (WGCNA) and m-fuzz clustering analysis reveals the overall and stage-specific lncRNA biotypes during cortical neuronal differentiation.

From: Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation

Fig. 1

A synopsis of lncRNA biotypes during cortical neuronal differentiation. a Percentage of lncRNA biotype-associated coding genes with ≥1 RPKM value during in vitro cortecogenesis. b Percentage of lncRNA biotype-associated coding genes significantly involved in neuronal differentiation as per the Gene Ontology database. c Change in the percentage of lncRNA biotype-associated coding genes during neuronal differentiation as compared with overall cortical differentiation. d–i Topological overlapping matrix generated using WGCNA on expression data of different lncRNA biotypes. Clustering is based on the comparison of overall corticogenesis with neurogenesis. Maximum numbers of lncRNA gene-forming clusters during neuronal differentiation belong to the XH biotypes, followed by IG, XI, and SD. While SU and XO do not show any cluster with significantly higher membership score. j–l M-fuzz clustering analysis of different lncRNA biotypes at different stages of cortical neuronal differentiation. The upper panel shows the expression association of different biotypes of lncRNA-associated genes with D0- (Pluripotency) stage markers (POU5F (OCT4), NANOG, NODAL, and TDGF). The clustering sharply drops from day 0 to day 7. The middle panel shows the expression association of different biotypes of lncRNA genes associated with D7- (neuronal commitment) stage markers (PAX6 and SOX1). Clustering has sharply increased from day 0 to day 7. The lower panel shows the expression association of different biotypes of lncRNA-associated genes with later development-stage markers (EMX2, TBR1, CTIP2, CACNA1E, PRSS12, and CARTPT). m The number of lncRNA biotype-associated genes enriched at different stages of cortical neuronal development. IG with a maximum number of genes involved, which are around 30 and at D0 and later development stage, respectively, while at D7, XH biotypes showing the maximum involvement that is around 30.

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