Table 1.
Gene expression studies of EMT used for meta-analysis.
Figure 1.
Cluster analysis of genes shared between at least 10 GES datasets shows distinguishable and significant clusters.
Genes shared between at least 10 out of 24 datasets were used for Manhattan hierarchical clustering. The type of regulation within a particular study was visualized via heatmap. Columns: genes shared between at least 10 datasets (n = 365); rows: analyzed GES (24 datasets in total); green: downregulated genes; red: upregulated genes; black: genes not regulated. GSE: Gene expression omnibus (GEO) series record; E.TABM: ArrayExpress (AE) series record; TGF, transforming growth factor; TNF, tumor necrosis factor.
Figure 2.
Gene expression studies cluster according to the mode of EMT initiation rather than to cell type.
The cell type and treatment modality of EMT was annotated and revealed clustering according to the mode of EMT induction. The clustering persisted when genes shared between at least 14 GES datasets were used for the analysis. (A) Hierarchical clustering of 365 genes shared between at least 10 datasets. (B) Hierarchical clustering of 41 genes shared between at least 14 datasets. The legend indicates cell type and treatment modality (right panel). *, Transcription factor vectors: Runx2, Six1, Snail, Twist and Goosecoid. GSE: Gene expression omnibus (GEO) series record; E.TABM: ArrayExpress (AE) series record; TGF, transforming growth factor; TNF, tumor necrosis factor.
Table 2.
EMT-core list of 130 genes shared between at least 10 GES datasets.
Figure 3.
The 130 genes EMT-core list and the 365 genes list exhibit comparable enrichment ratios of GO biological processes and KEGG pathways.
The enrichment ratio is the number of observed genes divided by the number of expected genes for a given term or pathway. Enrichment ratios were obtained from WebGestalt or calculated with data from FatiGO. GO, gene ontology; BP, biological process; KEGG, Kyoto encyclopedia of genes and genomes.
Table 3.
Number of enriched terms and pathways in all lists detected by the enrichment tools.
Table 4.
Consistently enriched GO terms and KEGG pathways and their occurrence in the analyzed gene lists.