Differentially expressed lncRNAs and protein coding genes in patients with Cerebral Cavernous Malformation (CCM)
Transcriptome profiles of CCM patients with differential expression patterns of LncRNAs and PCGs. (a) Heatmap showing differential expression of lncRNAs and PCGs between CCMs (n = 10) and control group (n = 4). (b) Volcano plots shows up- (red) and down-regulated (blue) lncRNAs and PCGs. Key significantly differentially expressed transcripts are highlighted with pink and known CCM related PCGs are highlighted with yellow. Vertical dotted lines represent log-fold change cut-off ±1.5 (right and left) and values above horizontal dotted lines represent transcripts with FDR <0.05 cut-off. (c) Kernal density graph showing coding potential probability of DE lncRNAs and DE PCGs. Probability or score is calculated using coding potential calculator (CPC). Green dotted lines divide coding and noncoding CPC scores. (d) Scatterplot shows DE lncRNAs and its number of correlated or co-expressed DE PCGs. Left side of the pink dotted line denotes DE lncRNAs (n = 326) having more than 100 correlated DE PCGs.
Co-expressed protein coding genes and pathways associated with top two CCM deregulated lncRNAs
Top lncRNAs LBX2-AS1 and SMIM25 co-expression network and its potential co-regulatory functions. (a) Network shows top two lncRNAs and co-expressed DE PCGs determined by its expression correlation. Nodes and edges in the network are generated using cytoscape. Venn diagram shows common DE PCGs co-expressed between top validated lncRNAs LBX2-AS1 and SMIM25. (b) Bar graph with enriched biological process, pathways and phenotypes derived using GeneSCF. Different color codes indicate terms derived from different database repositories. Gene ontology terms are denoted as red (Biological Process, BP), dark blue (Cellular components, CC) and yellow (Molecular Function, MF); KEGG pathways are in in purple; Reactome pathways are shown in green; and Human Phenotype Ontology terms as light blue. Enrichment in the scale denotes −log10 (p-value) and number above each bar represents number of genes.