Table 1.
Enrichment results for top cell type and lineage DEGs.
| Cell Type/Subtype | Process/Pathway a | Method | Expr | #DEGs b | Key Cell Type DEGs |
|---|---|---|---|---|---|
| D00 PP-A1A2 | OXPHOS | ORA | UNDER | 3 | DNAJC15, NDUFA3, NDUFA6 |
| D00 PP-B | Dosage compensation | ORA | UNDER | 1 | XIST (XL) |
| D09B CP-A | OXPHOS | GSEA | UNDER | 46 | Electron Transport Chain genes |
| Muscle dev/diff | ORA | UNDER | 2 | LMNA, NKX2-5 | |
| D09B CP-B | Epigenetic gene expr | ORA | UNDER | 2 | XIST (XL), NDN |
| Muscle/myofibril dev | ORA | OVER | 2 | KRT19, MYL9 | |
| D09B EPDC | Dosage compensation | ORA | UNDER | 1 | XIST (XL) |
| Glycolysis | ORA | OVER | 1 | PFKP | |
| D16 CM-A1A2 | TGF Beta signaling | GSEA | UNDER | 7 | SMAD6, ID1, ID2, ID3 |
| RSTK signaling | ORA | UNDER | 13 | ID1 | |
| Muscle contraction | ORA | UNDER | 8–11 | CACNA1D, CACNA1G | |
| Muscle development | ORA | UNDER | 13 | NKX2-5, WNT2 | |
| Glycolysis | GSEA | OVER | 27 | HK2, ENO2 | |
| OXPHOS | GSEA | OVER | 72 | Electron Transport Chain genes | |
| OXPHOS | ORA | OVER | 16 | Electron Transport Chain genes | |
| Myc targets | GSEA | OVER | 36 | Spliceosome genes x10, TYMS | |
| Muscle dev/diff | ORA | OVER | 23–31 | ACTC1, ACTN2, CSRP3, MYH7 | |
| EMT | GSEA | OVER | 23 | CDH2, TIMP1 (XL) | |
| D16 EPDC | mTORC1 signaling | GSEA | OVER | 43 | HK2, PGK1, ENO1, GAPDH, LDHA, PHGDH, SHMT2 |
| Nucleotide metabolism | ORA | OVER | 11–12 | PFKP, TPI1, PKM, GAPDH, TKT, HINT1, PAICS | |
| Precursor Metabolites | ORA | OVER | 12 | PFKP, TPI1, PKM, GAPDH, TKT | |
| D19 CM-A1 | Muscle differentiation | ORA | UNDER | 7–15 | LMNA, SYNPO2L, MYOZ2 |
| Myogenesis | GSEA | OVER | 37 | LDB3, MYBPC3, MYL2, MYL3, TCAP, TNNC1, TNNT2, DMD (XL) | |
| Muscle contraction | ORA | OVER | 14–21 | MYBPC3, MYL2, MYL3, TCAP, TNNI3 | |
| D19 EPDC | Epigenetic gene express | ORA | UNDER | 3 | LMNA, XIST (XL), NDN |
| Heterochromatin form | ORA | UNDER | 2 | LMNA, NDN | |
| Lineage | Process/Pathway a | Method | Expr | #DEGs b | Key Condition Test Lineage DEGs |
| PP Lineage: PP-A to PP-B |
Transcription | ORA | UNDER | 12 | Zinc-finger protein (ZNF) genes x10, HMBOX1, HEY2 |
| Metal homeostasis | ORA | OVER | 5–11 | MT1E, MT1F, MT1G, MT1H, BNIP3 | |
| CP Lineage-1: CP to CM |
Growth Factor response | ORA | OVER | 7 | GPC1, MT3, FOXD1, PMEPA1, CCBE1, DCN, SFRP5 |
| BMP signaling pathway | ORA | OVER | 4 | BMP4, GPC3 (XL), FST, LRP2 | |
| Metal homeostasis | ORA | OVER | 3 | MT1X, MT3, SLC39A4 | |
| CP Lineage-2: CP to EPDC |
Dosage compensation | ORA | UNDER | 1 | XIST (XL) |
| Cyclin kinase activity | ORA | OVER | 2 | CCNB2, CDKN3 |
a Enriched gene set using Cluster Profiler [62]: gene ontology biological process by ORA [64] or molecular signatures database Hallmark gene set by GSEA [61]. b Number (#) of DEG in enriched gene set by ORA or in leading edge subset by GSEA. Abbreviations: DEG, differentially expressed genes; expr, expression; PP, pluripotent; CP, cardiac progenitors; EPDC, epicardium-derived cells; CM, cardiomyocyte; OXPHOS, oxidative phosphorylation; dev, development; diff, differentiation; EMT, epithelial-mesenchymal transition; RSTK, receptor serine/threonine kinase; form, formation; ORA, over-representation analysis; GSEA, gene set enrichment analysis; UNDER, underexpressed; OVER, overexpressed; XL, X-linked.