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The identified modules need to be enriched with both eQTL genes and SCNA or mutated genes, with a corrected p <0.05.
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Most gene sets were enriched with both C/N DEGs and C/P DEGs.
For example, ECM genes were enriched with both DEX treatment and the day 15 micromass phenotype.
OCDB data is enriched with both validated and predicted miRNA-target and drug-target information.
Similarly, there are 24 pathways that were enriched with both C/N_up and C/P_up DEGs (Additional file 4, 5).
Twenty-one pathways were enriched with both C/N_down and C/P_down DEGs (Additional file 4, 5).
CMV promoter was enriched with both anti-H3K9 and anti-H3 diMeK4 antibodies at day 2 after transduction.
As has been found in other stem cell systems (Aloia et al., 2013), in SVZ cells, Ink4a was enriched with both H3K27me3 and the EZH2 methyltransferase.
At the same time, only one TFT "RGTTAMWNATT_V$HNF1_01" was enriched with both C/N_down and C/P_down DEGs (Additional file 4, 5).
The fifth cluster (8% of all genes) is enriched with both elongation (H3K36me3) and active marks (H3k9me1) but depleted of the canonical activating marks (H3k4me, H3k9ac, and H3k27ac).
We found 19 TFTs were enriched with both C/N_up and C/P_up DEGs (Additional file 4, 5), with the cell cycle controlling transcription factor E2F family being the most conspicuous factor.
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