Table 1.
Top 30 differentially expressed genes: MSC-γ versus UT-MSC.
| Gene symbol | Gene name | mRNA Accession | Fold change | p value |
|---|---|---|---|---|
| Upregulated genes | ||||
| HLA-DRA | Major histocompatibility complex, class II, DR alpha | NM_019111 | 387.78 | 0.00049 |
| GBP4 | Guanylate binding protein 4 | NM_052941 | 199.41 | 0.00002 |
| IDO1 | Indoleamine 2,3-dioxygenase 1 | NM_002164 | 96.72 | 0.00003 |
| HLA-DRB | Major histocompatibility complex, class II, DR beta | ENST00000307137 | 89.67 | 0.00435 |
| GBP5 | Guanylate binding protein 5 | NM_052942 | 88.07 | 0.00003 |
| CXCL9 | Chemokine (C-X-C motif) ligand 9 | NM_002416 | 83.60 | 0.00002 |
| GBP2 | Guanylate binding protein 2, interferon-inducible | ENST00000464839 | 77.00 | 0.00004 |
| SECTM1 | Secreted and transmembrane 1; NULL | NM_003004 | 57.59 | 0.00002 |
| HLA-DRB3 | Major histocompatibility complex, class II, DR beta 3 | ENST00000426847 | 51.65 | 0.00868 |
| CIITA | Class II, major histocompatibility complex, transactivator | NM_00024 | 38.84 | 0.00003 |
| GBP1 | Guanylate binding protein 1, interferon-inducible | NM_002053 | 29.09 | 0.00001 |
| RP11-44K6.2 | NULL | ENST00000520185 | 26.39 | 0.00060 |
| GCH1 | GTP cyclohydrolase 1 | NM_000161 | 24.93 | 0.00022 |
| USP30-AS1 | USP30 antisense RNA 1 | ENST00000478808 | 24.75 | 0.00009 |
| GBP2 | Guanylate binding protein 2, interferon-inducible; NULL | NM_004120 | 23.60 | 0.00001 |
| HLA-DOA | Major histocompatibility complex, class II, DO alpha; NULL | NM_002119 | 22.90 | 0.00003 |
| IFIT3 | Interferon-induced protein with tetratricopeptide repeats 3 | NM_001031683 | 21.49 | 0.00013 |
| FAM129A | Family with sequence similarity 129, member A | NM_052966 | 20.89 | 0.00003 |
| CTSS | Cathepsin S | NM_004079 | 20.10 | 0.00002 |
| SLC7A11 | Solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11 | NM_014331 | 19.70 | 0.00009 |
| IRF1 | Interferon regulatory factor 1 | NM_002198 | 19.55 | 0.00002 |
| CD74 | CD74 molecule, major histocompatibility complex, class II invariant chain; NULL | NM_001025159 | 18.49 | 0.00060 |
| ICAM1 | Intercellular adhesion molecule 1 | NM_000201 | 18.43 | 0.00003 |
| HCP5 | HLA complex P5 (nonprotein coding); NULL | ENST00000457127 | 18.15 | 0.00032 |
| LGALS17A | Charcot-Leyden crystal protein pseudogene | ENST00000412609 | 18.12 | 0.00038 |
| PARP14 | Poly (ADP-ribose) polymerase family, member 14 | NM_017554; | 17.05 | 0.00014 |
| RARRES3 | Retinoic acid receptor responder (tazarotene induced) 3 | NM_004585 | 17.00 | 0.00007 |
| WARS | Tryptophanyl-tRNA synthetase; NULL | NM_004184 | 16.49 | 0.00002 |
| IFIT2 | Interferon-induced protein with tetratricopeptide repeats 2 | NM_001547 | 16.43 | 0.00051 |
| TMEM140 | transmembrane protein 140 | NM_018295 | 16.08 | 0.00012 |
| Downregulated genes | ||||
| LRRC15 | Leucine rich repeat containing 15 | NM_001135057 | −19.91 | 0.0007 |
| KIAA1199 | KIAA1199; NULL | NM_018689 | −13.26 | 0.0025 |
| RNU5A-8P | RNA, U5A small nuclear 8, pseudogene | ENST00000364102 | −12.36 | 0.0061 |
| COL10A1 | Collagen, type X, alpha 1 | NM_000493; | −12.25 | 0.0031 |
| COL3A1 | Collagen, type III, alpha 1; microRNA 3606 | NM_000090 | −11.88 | 0.0000 |
| HIST1H2A | Histone cluster 1, H2ai; histone cluster 1, H2ah; histone cluster 1, H2ag; histone cluster 1, H2am; histone cluster 1, H2al; histone cluster 1, H2ak; histone cluster 1, H3f | NM_003509 | −11.67 | 0.0012 |
| SCD | Stearoyl-CoA desaturase (delta-9-desaturase) | NM_005063 | −9.75 | 0.0000 |
| U2 | U2 spliceosomal RNA | ENST00000410792 | −9.41 | 0.0476 |
| HIST1H3 | Histone cluster 1, H3b; histone cluster 1, H3f; histone cluster 1, H3h; histone cluster 1, H3j; histone cluster 1, H3g; histone cluster 1, H3i; histone cluster 1, H3e; histone cluster 1, H3c; histone cluster 1, H3d; histone cluster 1, H3a | NM_003537 | −9.06 | 0.0053 |
| HIST1H1B | Histone cluster 1, H1b | NM_00532 | −8.53 | 0.0002 |
| — | — | ENST00000408768 | −8.25 | 0.0001 |
| KDELR3 | KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 | NM_016657 | −8.22 | 0.0007 |
| — | — | BC091525 | −7.87 | 0.0007 |
| SNORD114-11 | Small nucleolar RNA, C/D box 114-11 | NR_003204 | −7.33 | 0.0021 |
| WISP1 | WNT1 inducible signaling pathway protein 1 | NM_003882 | −7.18 | 0.0000 |
| U3 | Small nucleolar RNA U3 | ENST00000390893 | −7.14 | 0.0128 |
| HIST1H2BM | Histone cluster 1, H2bm | NM_003521 | −6.92 | 0.0024 |
| COL1A1 | Collagen, type I, alpha 1; NULL | NM_000088 | −6.84 | 0.0000 |
| HIST1H3 | histone cluster 1, H3g; histone cluster 1, H3f; histone cluster 1, H3b; histone cluster 1, H3h; histone cluster 1, H3j; histone cluster 1, H3i; histone cluster 1, H3e; histone cluster 1, H3c; histone cluster 1, H3d; histone cluster 1, H3a | NM_003534 | −6.68 | 0.0032 |
| HIST1H3 | Histone cluster 1, H3f; histone cluster 1, H3b; histone cluster 1, H3h; histone cluster 1, H3j; histone cluster 1, H3g; histone cluster 1, H3i; histone cluster 1, H3e; histone cluster 1, H3c; histone cluster 1, H3d; histone cluster 1, H3a | NM_021018 | −6.41 | 0.0058 |
| AL732479.1 | — | ENST00000459197 | −6.38 | 0.0015 |
| ADAM12 | ADAM metallopeptidase domain 12; NULL | NM_003474; | −6.13 | 0.0001 |
| ENPP1 | Ectonucleotide pyrophosphatase/phosphodiesterase 1 | NM_006208 | −6.06 | 0.0002 |
| NDNF | Neuron-derived neurotrophic factor | NM_024574 | −6.00 | 0.0100 |
| DHCR7 | 7-Dehydrocholesterol reductase; NULL | NM_001360 | −5.88 | 0.0005 |
| DHCR24 | 24-Dehydrocholesterol reductase | NM_014762 | −5.84 | 0.0001 |
| RGS4 | Regulator of G-protein signaling 4; NULL | NM_001102445 | −5.78 | 0.0116 |
| CRABP2 | Cellular retinoic acid binding protein 2 | NM_001878 | −5.76 | 0.0015 |
| KIF20A | Kinesin family member 20A; NULL | NM_005733 | −5.60 | 0.0072 |
| U1 | U1 spliceosomal RNA | — | −5.38 | 0.0069 |