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Table 1 Functional enrichment on KEGG signaling pathways of MSCs expressed coding genes

From: Transcriptomic portrait of human Mesenchymal Stromal/Stem cells isolated from bone marrow and placenta

KEGG pathway

Gene set size

Observed hits

Adjusted p-value*

Hits (Gene_Symbols)

mTOR signaling pathway (hsa04150)

52

27

0.0000505

AKT1, AKT3, CAB39, CAB39L, EIF4E2, EIF4EBP1, MAPK1M MAPK3, MLST8, MTOR, PIK3CB, PIK3R2, PRKAA1, PRKAA1, RHEB, RPS6, RPS6KA2, RPS6KA3, RPS6KB1, RPS6KB2, STK11, TSC1, TSC2, ULK1, ULK3, VEGFA, VEGFB, VEGFC

ErbB signaling pathway (hsa04012)

87

35

0.0019942

ABL1, AKT1, AKT3, BAD, CDKN1A, CDKN1B, CRK, CRKL, EGFR, EIF4EBP1, ELK1, ERBB2, GRN2, GSK3B, HBEGF, HRAS, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK3, MAPK8, MAPK9, MTOR, MYC, NCK2, NRAS, PAK1, PAK2, PIK3CB, PIK3RS, RPS6KB1, RPS6KB2

TGF-beta signaling pathway (hsa04330)

83

33

0.0032629

BMPR1A, BMPR2, CDKN2B, CUL1, E2F4, ID1, ID3, MAPK1, MAPK3, MYC, PPP2CB, PPP2R1A, PPP2R1B, RBL2, RBX1, ROCK1, ROCK2, RPS6KB1, RPS6KB2, SKP1, SMADA, SMAD4, SMAD7, SMURF2, SP1, TFDP1, TGFB2, TGFBR1, TGFBR2, THBS2, ZFYVE16, ZFYVE9

Notch signaling pathway (hsa04330)

46

20

0.0056174

ADAM17, APH1A, CIR1, CTBP1, CTBP1, CTBP2, DTX3, DTX3, DTX3L, DVL1, DVL2, HDAC1, HDAC1, HDAC2, HES1, NCOR2, NOTCH2, NOTCH3, NUMB, NUMBL, PSEN2, RBPJ, RFNG

Osteociast differentiation (hsa04380)

127

45

0.0088651

AKT1, AKT3, CHUK, CYBA, FHL2, FOS, FOSB, FOSB, FOSL1, FOSL2, GRB2, IFNAR1, IFNAR2, IFNGR1, IFNGR2, IFNGR2, IKBKB, IRF9, JAK1, JUNB, JUND, MAP2K1, MAP2K7, MAP2K7, MAP3K7, MAPK1, MAPK12, MAPK14, MAPK3, MAPK3, MAPK8, MAPK9, NFKBIA, PIK3CB, PIK3R2, PP3CA, PPP3CC, RAC1, RELA, SIRPA, SOCS3, SQSTM1, STAT2, TAB2, TGFB2, TGFBRI, TGFBR2, TNFRSF11B, TYK2

Wnt signaling pathway (hsa04310)

150

51

0.0134525

CCND1, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, DVL1, DVL2, FOSL1, FZD2, FZD4, FZD6, FZD7, FZD8, GSK3B, LRP5, LRP6, MAP3K7, MAPK8, MAPK9, MYC, PLCB3, PPP2R5C, PPP2RSE, PPP3CA, PPP3CC, PPP3R1, PRICKLE1, SENP2, SFRP4, SIAH1, SKP1, SMAD2, SMAD4, TCF7L1, WNT5B

Apoptosis (hsa04210)

87

32

0.0136314

AIFM1, AKT1, AKT3, BAD, BAX, BCL2L1, BID, BIRC2, CAPN1, CAPN2, CASP6, CASP8, CAPSP9, CFLAR, CHUK, ENDOG, FADD, IKBKB, IRAK1, NFKBIA, PIK3CB, PIK3R2, PPP3CA, PPP3CC, PPP3R1, PRKACA, PRKAR1A, RELA, RIPK1, TNFRSF10D, TRADD, XDIAP

VEGF signaling pathway (hsa04370)

75

28

0.0160140

AKT1, AKT3, BAD, CASP9, CDC42, HRAS, HSPB1, KRAS,

Adipocytokine signaling pathway (hsa04920)

67

25

0.0207573

ACSL1, ACSL3, ADIPOR1, ADIPOR2, AKT1, AKT3, CHUK, CPT1A, IKBKB, MAPK8, MAPK9, MAPK9, MTOR, NFKBIA, NFKBIB, PCK2, PRKAA1, PRKAB1, PRLAB2, PRKAG1, PTPN11, RELA, SOCS3, STAT3, STK11, TRADD

  1. *Hypergeometric test (p-values adjusted using Benjamini and Hockberg method; done with HTSanalyze R-pakage).