Table 2.
Top ten upregulated genes in control clusters.
| Cluster | Parameter | Fold-change | FDR q-value |
|---|---|---|---|
| 2 | TOP2A | 28.61185732 | 3.55E−231 |
| 2 | MKI67 | 26.27793419 | 0 |
| 2 | NEK2 | 24.64180751 | 8.94E−89 |
| 2 | CENPF | 23.20713437 | 1.3024430098599E−317 |
| 2 | NUF2 | 22.46846048 | 9.23E−136 |
| 2 | SPC25 | 21.06233128 | 1.27E−129 |
| 2 | KIF15 | 20.71534477 | 1.20E−67 |
| 2 | PSRC1 | 20.18222113 | 1.46E−64 |
| 2 | KIF18A | 20.14262227 | 1.11E−47 |
| 2 | CKAP2L | 19.99418063 | 2.34E−112 |
| 6 | RASGRP3 | 10.13670085 | 6.27E−88 |
| 6 | CXCR4 | 8.520098363 | 2.00E−299 |
| 6 | CD200 | 5.158937263 | 1.57E−17 |
| 6 | CSGALNACT1 | 5.173452832 | 5.44E−116 |
| 6 | CHST1 | 10.93093523 | 4.56E−166 |
| 6 | DEPP1 | 9.216096628 | 2.72E−259 |
| 6 | MGP | 6.676951416 | 5.00E−138 |
| 6 | RGCC | 5.174688626 | 2.54E−231 |
| 6 | NID2 | 5.645609732 | 2.07E−26 |
| 6 | PLA2G4C | 6.073089562 | 5.78E−105 |
| 7 | HLX | 3.308916449 | 4.14E−16 |
| 7 | NOTCH4 | 2.994194879 | 1.03E−31 |
| 7 | AKAP12 | 3.897821175 | 7.75E−57 |
| 7 | PEG10 | 3.317471895 | 3.69E−28 |
| 7 | APLN | 3.051646077 | 8.94E−49 |
| 7 | CNTNAP3B | 3.478569887 | 5.03E−47 |
| 7 | PGF | 3.46250528 | 6.01E−113 |
| 7 | YPEL2 | 2.966003011 | 1.13E−21 |
| 7 | LIPG | 3.10185442 | 1.08E−09 |
| 7 | PDGFB | 2.983750339 | 8.70E−17 |
| 8 | PTX3 | 2.383583031 | 4.29E−82 |
| 8 | DDIT4L | 2.344600929 | 2.83E−11 |
| 8 | HHIP | 2.314530069 | 7.29E−125 |
| 8 | TGFBI | 2.439371111 | 9.35E−25 |
| 8 | PLAT | 2.945899196 | 2.15E−40 |
| 8 | FRMD3 | 2.432868258 | 6.78E−14 |
| 8 | CLIC3 | 2.445455159 | 0.002293661 |
| 8 | ANKRD1 | 2.490652973 | 5.36E−48 |
| 8 | ITGB3 | 2.343396353 | 6.43E−28 |
| 8 | FSTL3 | 2.403705182 | 9.46E−15 |
Clusters 1 and 3–5 among control PAEC exhibited mostly down-regulated genes. The set of top ten overexpressed genes in control 2 cluster was enriched in genes involving cell proliferation, including cenpf, ckap2l, kif15, kif18a, mik67, nek2 and spc25. Control cluster 6 had increased expression of top ten genes regulating immune cell—endothelial interaction and new vessel formation such as cd200, Carbohydrate Sulfotransferase 1 (chst1), cxcr4, matrix Gla protein (mgp), and Ras guanyl-releasing protein 3 (rasgrp3). Sprouting and migratory gene signatures, A-kinase anchoring protein 12 (akap12), aplin (apln), H2. 0 Like Homeobox (hlx), Neurogenic locus notch homolog 4 (notch4), and pdgfb were enriched in control cluster 7. Highly expressed genes in control cluster 8 were characteristic of inflammation and angiogenesis, including fstl3, hhip, itgb3, ptx3 and tgfb1.