TABLE 1.
Selected Ontologies Significantly Associated With the Response to TGFβ Treatment in Mesenchymal Cells Derived From Human Intestinal Organoids
| Pathway | q Value | Regulated/Total | Upregulated by TGFβ | Downregulated by TGFβ |
|---|---|---|---|---|
| Epithelial-mesenchymal transition | 1 × 10-68 | 92/200 | ACTA2, ADAM12, ADAM19, ADAMTS10, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, AEBP1, ANOS1, APLP1, B4GALT1, BGN, CALD1, CCN2, CDH11, CDH2, CILP2, CILP, CILP2, COL10A, COL11A1, COL12A1, COL16A1, COL1A1, COL24A, COL25A1, COL3A1, COL4A1, COL4A2, COL5A1, COL5A2, COL6A3, COL7A1, COL8A1, COL8A2, COL9A2, COMP, CREB3L1, CRISPLD2, CRLF1, DKK1, DPT, ELN, EMILIN1, MFAP4, MFAP2, FAP, CFAP44, MFAP3L, FBLN5, FBN1, FERMT2, FN1, FNDC1, FSTL3, FZD8, GADD45B, GPX7, GREM1, HAPLN3, HMCN1, IGFBP3, IGFBP7, INHBA, ITGA1, ITGA11, ITGA11, ITGA8, ITGAV, ITGB1BP2, ITGB1, ITGB3, ITGB5, ITGB6, JUNB, KAZALD1, LAMC2, LOX, ALOX5AP, LOXL3, LOXL3, LRP12, LRP1, LRRC15, LTBP1, LTBP2, MATN3, MFAP2, MFAP4, MMP16, MMP2, MXRA5, MYL9, P3H1, P3H4, P4HA1, P4HA2, P4HA3, PDGFA, PHLDB1, PLOD1, PMEPA1, PODNL1, PODNL1, POSTN, PRG4, RUNX1, PSAT1, SCX, SDC1, SERPINE2, SERPINH1, SGCD, SGCG, SH3PXD2A, SPARC, SRPX2, TAGLN, TGFB1, TGFB3, TGFBI, TGM2, THBS1, TIMP3, TNC, TNFAIP6, TPM1, TPM2, VCAN | ANPEP, BMPER, COL21A1, COL4A6, CRISPLD1, CXCL16, CXCL1, CXCL6, CXCL8, DAB2, DCN, EFEMP1, AFAP1L2, TFAP4, GAS1, IGFBP4, IGFBP6, IGSF10, IL15, IL32, ITGA10, JUN, LAMA4, MATN2, MCM7, MEST, NTN1, NTN4, NTNG1, OXTR, PAPLN, PODN, PRELP, PTX3, RGS4, SAT1, SDC4, SFRP1, SLIT2, SNTB, SRGN, SVEP1, TGFBR3, THSD4, VCAM1, VWA5A, VWCE |
| ECM organization | 1 × 10-45 | 71/395 | ||
| ECM glycoproteins | 1 × 10-20 | 48/196 | ||
| Interferon signaling | 1 × 10-28 | 46/200 | IFITM10 | ANPEP, APOBEC3B, APOBEC3F, APOBEC3G, BST2, C1RL, C1R, CAMK2D, CASP4, CAV1, CCL2, CDK18, CDK1, CFH, CLDN11, CLDN1, CSF1, CXCL6, CXCL8, DCLK1, DDX58, DDX60, DHX58, DPP4, DTX3L, EGFR, F2RL1, FAM111A, FOSL1, HELZ2, HERC6, HMGA1, HMGA2, ICAM1, IFI16, IFI35, IFI44, IFI6, IFIH1, IFIT1, IFIT2, IFIT3, IFIT5, IFITM1, IFITM2, IFITM3, IL15, IRF1, IRF2, ITGB8, LGALS3BP, MID1, MX1, NEDD4L, NFIA, NMI, NRP1, OAS3, PARP10, PARP12, PARP14, PARP9, PLSCR1, POLR3G, PSMB8, PSMB9, PSME1, PTX3, SAMHD1, SECTM1, SLC20A2, SOCS1, SOCS3, SOD2, SP110, STING1, STMN1, STOM, TNFAIP2, TNFSF10, TRIM14, TRIM25, TXNIP, UBE2L6, USP18, VCAM1, VWCE |
| Cell cycle | 1 × 10-30 | 45/200 | ASF1B, ATAD2, AURKA, BRCA1, BUB1B, CDC25A, CDC25B, CDC45, CDCA3, CDCA8, CDK18, CDK1, CENPM, CHAF1A, CITED2, CIT, CKS1B, CKS2, E2F1, EFNA5, EXO1, GINS1, GINS2, GINS3, GINS4, HELLS, HMGA1, HMGB2, KIF11, KIF15, KIF20B, KIF22, LMNB1, MAD2L1, MCM2, MCM3, MCM4, MCM5, MCM7, MELK, MXD3, NEK2, ORC6, PBK, PRIM2, RACGAP1, RAD51AP1, RAD54L, RBL1, RFC3, RNASEH2A, RRM2, SAP30, SHMT1, SMAD3, SPC24, STMN1, TACC3, TCF19, TIMELESS, TK1, TPX2, TRAIP, TRIP13 | |
| Response to TGFβ | 1 × 10-17 | 50/261 | CDKN2B, CHST11, CILP2, CILP, COL1A1, COL3A1, COL4A2, DKK3, EMILIN1, FBN1, FERMT2, ID1, ITGB1BP2, ITGB1, ITGB5, ITGB6, JUNB, LOX, ALOX5AP, LOXL3, LRRC32, LTBP1, LTBP2, MXRA5, MYOCD, NOX4, PMEPA1, POSTN, RASL11B, SCX, SKIL, SMAD7, SNX25, TGFB1, TGFB3, THBS1 | CAV1, CITED2, CLDN11, CLDN1, CLEC3B, DAB2, GDF5, HTRA3, MID1, ITGB8, JUN, PDE3A, PDGFD, PEG10, SFRP1, SMAD1, SMAD3, SPRY1, TGFBR2, TGFBR3, ZFP36L2 |
Specific terms were selected from the summary enrichment shown in Figure 3. Shown are the individual hypergeometric q values for each ontology, the number of genes significantly regulated by TGFβ regardless of source (induced pluripotent stem cell line) along with the total number of human genes annotated in each ontology (regulated/total), and official gene symbols for both up and downregulated genes after treatment with TGFβ.
Abbreviations: ECM, extracellular matrix; TGFβ, transforming growth factor β.