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Table 2 Functional enrichment analysis of DE genes obtained from the meta-analysis approach

From: Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

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

  1. 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