Fig. 3: Directional integration of transcriptomics data from functional experiments of HOXA10-AS lncRNA in GBM cells.

A We integrated differential gene expression data from HOXA10-AS knockdown (KD) and overexpression (OE) experiments from a previous study²⁷ that compared sets of three replicates. DPM prioritised genes that showed different fold-change (FC) directions in KD and OE experiments and penalised genes with matching directions using the constraints vector (CV) [KD = −1, OE = +1]. B Scatter plot of merged P-values from directional analysis (DPM, Y-axis) and non-directional analysis (the Brown method, X-axis). Prioritised genes with directionally consistent changes are shown on the diagonal or closely below it (blue), while directionally penalised genes with conflicting directional changes are further below the diagonal (red). Unadjusted P-values are shown. C Examples of prioritised genes (top) and penalised genes (bottom). D Venn diagram of enriched pathways found with directional and non-directional analyses (family-wise error rate (FWER) < 0.05). E Enrichment map of pathways and processes from directional and non-directional analyses (FWER < 0.05). Pathways are shown as node in the network that are connected by edges if the pathways share many genes. Subnetworks represent functional themes. Node colours indicate dataset contributions (KD, OE, both, or combined-only). Node size reflects number of genes per pathway. Node outlines show directionally prioritised pathways (spiky edges), directionally penalised pathways (dotted edges), or pathways found using both approaches (solid edges). Major groups of directionally prioritised or penalised pathways are grouped on the right. F Dot plots of significant genes involved in cell migration and oxygen response processes visualised with P-values and fold-change values from the HOXA10-AS transcriptomics study²⁷. Genes penalised in the non-directional analysis are indicated with asterisks. Carets show known cancer genes from the COSMIC Cancer Gene Census database⁵³.