Table 2.
Functional enrichment analysis of DE genes obtained from the meta-analysis approach
| Annotation term | Hits (gene symbols) | Hits | Term hits (%) | Adj.p-val (Benjamini) |
|---|---|---|---|---|
| Enriched functions in 2124 genes overexpresed in BM-MSCs compared to HSPCs | ||||
| cytoplasmic membrane-bounded vesicle | SEPT5, TGOLN2, SEC31A, FSTL3, ITSN1, C14ORF1, APP, BDNF, DAB2, PICALM, SCAMP1, BSG, MYO6, ACTN1, OPTN, SSPN, SPAG9, VEGFC, SERPINF1, RAB14, TRAPPC4, PDCD6IP, COPZ2, CAV2, RAB7A, PAM, COPZ1, ATP6V1B2, ITGB1, CALU, TIMP1, STX12, SLC30A5, TMED10, FN1, AP2M1, PLAT, P4HB, BECN1, GARS, WIPI1, DVL1, LAMP1, LAMP2, PPIB, YIPF3, YIPF5, HSP90AB1, COPA, CLTA, CLTB, SEC24A, RAB5B, AP2S1, HEXB, AP3S1, GJA1, PDIA6, PDIA4, CLTC, CANX, RABAC1, SLC1A5, COPB2, AP2B1, TPP1, MAPKAP1, GOPC, GOLGA5, ATP6V0D1, SEC24D, STX6, SEC23A, ADAM10, STX2, PIK3C2A, STXBP1, TMEM187, BGN, IGF2R, ARCN1, RAB5A, SORT1, CTSD, CTSB, COPG, COPE, GANAB, ANXA6, CD9, TMED2, CRISPLD2, TMEM33, CAMK2D, RAB11A, SNAP23, GPNMB, THBS1, EHD1, THBS2, EHD3, HSPA8, THBS3, PHLDA1, YWHAB, SPARC, TMEM168, ANXA2, NCSTN, SH3BP4, SCFD1, HSP90B1, LRP1, SMPD1 | 114 | 5.73 | 8.84E-07 |
| establishment of vesicle localization | SEPT5, BBS4, COPA, MAP2K1, BBS7, COPZ1, WIPI1, COPB2, ARF1, PSEN1, ARCN1, TMED10, SNAP23, COPG, YKT6, COPE | 16 | 0.80 | 1.72E-04 |
| blood vessel development | RTN4, NRP1, HTATIP2, PGF, PRRX1, ANPEP, MMP2, CXCL12, CITED2, MAP3K7, AKT1, SHB, ATG5, CTGF, ANG, ROBO1, SEMA3C, RHOB, LOX, NR2F2, FGF2, CYR61, RECK, MYH9, SLIT2, THY1, VEGFC, BGN, HIF1A, NUS1, PSEN1, COL1A2, FOXC1, COL1A1, ACVR1, CAV1, TNFRSF12A, COL3A1, CDH2, TCF7L2, SEMA5A, PTK2, ITGAV, CHM, THBS1, PPAP2B, C1GALT1, RASA1, PLAT, EPAS1, MYO1E, TGFBR2, COL5A1, ANXA2, CDH13, GPI, LAMA4, PKNOX1, ENG, PLAU | 60 | 3.02 | 5.06E-06 |
| apoptosis | DLC1, TSPO, HRAS, MEF2A, SGMS1, ITSN1, MAGED1, SHB, CLPTM1L, APP, CDKN2A, RAD21, ATG5, UNC5B, GATA6, FAS, DAP, CUL1, CIB1, TWIST1, FADD, LIG4, BCAP31, PDCD6IP, NEK6, BLCAP, TNFRSF12A, RRAGA, BCL2L2, STK17A, RRAGC, PEA15, PRUNE2, DOCK1, TCTN3, ABR, TM2D1, LGALS1, SRA1, TRIO, FXR1, VDAC1, NCKAP1, BFAR, VCP, RABEP1, RTN4, HTATIP2, SGPP1, ZMAT3, BNIP3, GJA1, PAWR, DAXX, RTN3, AKT1, TNFRSF11B, DYNLL1, PAK2, BOK, GSN, BAG3, BAG2, RHOB, FGF2, MYC, MAGEH1, NDUFS1, DHCR24, LTBR, NOL3, ARHGEF12, CDK5, ECT2, ELMO2, ZDHHC16, EYA2, PSEN1, AVEN, PSME3, UBE2Z, ITM2B, GLRX2, TNFRSF1A, BCAP29, THBS1, PHLDA3, PHLDA2, ERCC2, PHLDA1, ACTC1, IL6, DNM1L, TMBIM6, UBE4B, YWHAB, BAD, STAT1, PLEKHF1, NCSTN, BNIP3L, SULF1, PERP | 103 | 5.18 | 2.75E-03 |
| cell migration | CTHRC1, JUB, NRP1, CXCL12, CTGF, ANG, ROBO1, SEMA3C, CAP1, NR2F2, FGF2, TWIST1, PRKCA, PTPRK, SATB2, ARID5B, EMX2, NRD1, MYH9, CDK5, SLIT2, VEGFC, HIF1A, TNS1, PSEN1, CFL1, SIX1, PDGFRB, FOXC1, LAMC1, ACVR1, CAV2, CCL2, NDN, FUT8, TNFRSF12A, ITGA11, KITLG, CDH2, ITGB1, VCAM1, PTK2, PAFAH1B1, PPAP2A, THBS1, PPAP2B, APC, FN1, PLAT, IL6, MET, COL5A1, CDH13, FYN, ITGA5, LRP6, APBB2, ENG, PLAU, MYH10 | 60 | 3.02 | 2.36E-04 |
| Enriched functions in 2624 genes overexpressed in HSPCs compared to BM-MSCs | ||||
| regulation of leukocyte activation | LST1, HMGB3, BLM, STAT5A, IL18, SNCA, SPINK5, SART1, CD74, ADA, IL31RA, IL1B, MS4A2, IL2RG, INPP5D, HLA-DOA, TRAF6, LAG3, CD28, SYK, FCER1A, PTPRC, IL2RA, GIMAP5, IKZF1, FLT3, SLA2, CTLA4, STXBP2, IDO1, NFAM1, PRKCQ, CD38, CD83, CORO1A, CD86, TNFSF13B, LAX1, PRAM1, RIPK2, IRF4, VSIG4, SASH3 | 43 | 1.92 | 9.33E-04 |
| hemopoiesis | LMO2, STAT5A, JAG2, TPD52, IL31RA, CDC42, SYK, RHOH, MB, EGR1, TTC7A, LYN, EOMES, NFAM1, DHRS2, CD40LG, AICDA, ADD2, CALCR, GPR183, BLM, KIT, ZBTB16, SOX6, TRIM10, CD74, ADA, TAL1, DOCK2, CHD7, RASGRP4, BCL2, BCL11A, TRAF6, CD28, PTPRC, GIMAP5, IKZF1, PLEK, EPB42, FLT3, HCLS1, HDAC5, HOXB4, RPL22, PLCG2, IRF8, IRF1, IRF4, SPTA1, CD79A, KLF1 | 52 | 2.33 | 6.28E-03 |
| positive regulation of T cell activation | PTPRC, IL2RA, GIMAP5, IKZF1, BLM, STAT5A, IL18, ADA, CD74, SART1, CD83, PRKCQ, CORO1A, CD86, TNFSF13B, RIPK2, IL1B, IL2RG, TRAF6, SASH3, CD28, SYK | 22 | 0.98 | 2.44E-02 |
| Enriched functions in 194 genes overexpressed in skin fibroblasts compared to BM-MSCs | ||||
| extracellular matrix | EGFL6, LGALS1, MMP27, GRIA3, EMILIN2, MMP3, NTN1, MMP1, WNT2, FBLN2, FBLN5, F3, FBN2, MFAP4 | 14 | 7.57 | 5.22E-03 |
| calcium ion binding | S100A4, F10, MASP1, LDLR, EGFL6, SCUBE2, MMP27, COLEC12, GALNTL1, MMP3, SLIT2, MMP1, DCHS1, STAT2, NPTX1, FBLN2, SVIL, FBLN5, ANXA11, CCBE1, FBN2, MFAP4, GALNT14 | 23 | 12.43 | 2.06E-02 |
| EGF-like, type3 | F10, LDLR, EGFL6, SCUBE2, FBLN2, FBLN5, CCBE1, ADAM33, FBN2, SLIT2 | 10 | 5.41 | 1.44E-02 |
| Enriched functions in 207 genes overexpressed in BM-MSCs compared to skin fibroblasts | ||||
| system development | INHBA, RBP4, CTGF, DLX5, CHST11, FHL2, SORT1, MGP, FOXC1, NPR3, COL5A2, ANKH | 12 | 6.32 | 5.08E-01 |
| Z disc | SORBS2, PDLIM5, DMD, FHL2, HOMER1 | 5 | 2.63 | 2.77E-01 |
| myofibril | SORBS2, PDLIM5, DMD, FHL2, HOMER1, TPM1 | 6 | 3.16 | 2.24E-01 |
Annotation Term: name and identifier of the annotated term in a functional database. Hits: (Observed Hits) number of genes from the DE gene list in each specific annotation term. Adj.p-val: (Adjusted p-values) p-values from functional enrichment analysis were adjusted using the Benjamini and Hochberg method. Gene symbols: identifiers of genes asigned to each functional term. Analyses were performed using DAVID web tool