Disease table of OSTEOPOROSIS OMIM ID: 166710

Gene-disease associations table

Gene	Associated with OSTEOPOROSIS in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
PDLIM4	OMIM	HGNC link	5q31.1	2	166710, 613418
VDR	OMIM	HGNC link	12q13.11	2	166710, 277440
LRP5	ClinVar, OMIM	HGNC link	11q13.2	9	144750, 166710, PS133780, PS174050, 601884, 173900, 607636, 259770, PS607634
CALCR	OMIM	HGNC link	7q21.3	2	166710, 613418
COL1A2	ClinVar, OMIM	HGNC link	7q21.3	4	166710, PS166200, 225320, 130060
COL1A1	OMIM	HGNC link	17q21.33	5	166710, 130000, PS166200, 114000, 130060
WNT1	HUMSAVAR	HGNC link	12q13.12	3	166710, 615221, PS166200

Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By sub-band

Shared sub_band	Number of genes associated with the disease	Genes associated with the disease
7q21.3	2	CALCR, COL1A2

By band

Shared band	Number of genes associated with the disease	Genes associated with the disease
12q13	2	WNT1, VDR
7q21	2	CALCR, COL1A2

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
12q1	2	WNT1, VDR
7q2	2	CALCR, COL1A2

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
12q	2	WNT1, VDR
7q	2	CALCR, COL1A2

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
12	2	WNT1, VDR
7	2	CALCR, COL1A2

Transcription Factors (TF) annotation from TRRUST

TF	associated to this disease	# regulated genes	Regulated genes	# regulated genes associated with this disease	Regulated genes associated with this disease
VDR	YES	36	DKK4, CST5, PRL, LRP5, IGFBP3, BGLAP, EGFR, TPT1, IL12B, SKP2, PHB, CYP7A1, RUNX2, TNFRSF21, CYP1A1, ERBB2, CD14, CYP24A1, CYP3A4, CDKN1B, FOXP3, PODXL, IL10, HOXA10, CDH1, CALB1, SPP1, AMH, TRPV6, DDIT4, CXCL8, IL2, PTH, IL6, CAMP, TNFSF11	1	LRP5
CIITA	NO	30	IRF2, HDAC2, COL1A2, HLA-DRB4, HLA-DRB1, HLA-DRB3, HLA-DRA, IL4, HLA-DMA, HLA-C, SIRT1, HLA-DQB1, HLA-B, SLC26A3, HLA-A, PLXNA1, COL1A1, HLA-DMB, HLA-DRB5, S100A4, MMP9, IRF1, PSMC5, HLA-DOB, HLA-DOA, HLA-DPB1, HLA-G, RAB4B, CREBBP, FASLG	2	COL1A2, COL1A1
NFKB1	NO	306	NRF1, VWF, FTH1, PGLYRP2, CDK4, RGS4, IFNG, MMP2, DCST1, AGT, THBD, EGFR, GDNF, CCL4, NCAM1, VEGFA, CR2, CFI, TP53, FOXO3, CYP19A1, BGN, LPL, CXCL12, ELF3, PTHLH, HOXA9, IRF7, TNC, AGER, EDN1, HBEGF, SFTPA1, SAA1, TSLP, GSK3A, IFNB1, GKN2, TRAF2, PLA2G2A, F3, IL10, LIPE, FAF1, IL17A, CEACAM1, AKT1, KLK3, IL1RN, GSTP1, E2F1, CCR5, TAPBP, ADORA2A, CXCL1, PTPN6, MMP3, PIGR, ERAP1, YY1, OLFM4, DEFB4A, CCL2, CD28, SQSTM1, TERT, IL4, NAMPT, BACE1, JUNB, SLC9A2, FASLG, ALOX5, BCL2L1, CD83, TLR3, CCL22, PLIN1, CDKN1A, BIRC3, CSF2, CFLAR, TFPI2, MYB, IL18, SERPINB1, MUC17, TNFRSF10A, PTGFR, TFF3, PTAFR, PTGS2, COX1, SERPINA3, ITGAX, CCND2, MCL1, TLR7, POU2F2, REPS2, CD3G, TFF1, B2M, PLAU, TNF, FOXP3, HDAC7, MUC5B, CCR2, FIGF, HSD11B2, CCL13, IFNA1, NOX5, MAT2A, COL7A1, HMOX1, ADORA1, TNFSF10, AR, COL2A1, TAP1, IL1B, CD74, CD38, MUC5AC, MUC2, TIMP1, CCL19, FGF8, PDK4, CCL20, STK39, CYP3A7, MMP9, GATA3, IRF4, CD58, HES1, PLAUR, SP4, NFKB1, MMP1, NOX4, BDKRB1, CASP3, CYP1A1, PSMB9, PTEN, HPSE, CCNB1, CD40, NOS3, PTGDS, UPP1, HIF1A, TNFRSF9, CD80, TNFSF13B, IL23A, TNFAIP3, TNFSF14, IL12A, TRPC1, CYP2E1, OPRM1, HLA-F, AMH, XIAP, MADCAM1, HYAL1, A2M, CCL11, TBX21, ICAM1, BCL2L11, CHUK, TAP2, IL2RA, CTCF, ABCB1, GSK3B, CCND1, KLF5, CCR7, CCK, DCST2, MMP14, IL17C, FBP1, OPTN, IL1A, LTC4S, COL1A2, NOS1, WT1, BIRC5, PPIG, PTGES, CREB3, CXCL2, CRP, KDM2A, BCL2A1, BRCA2, IKBKB, GFAP, PSMB10, PROX1, COL1A1, TNIP3, NFKBIZ, TLR2, S100A6, DRD2, CXCL8, CD86, TRAF1, PTPN13, CSNK2A1, CARD8, CXCL10, IL6, CFTR, CASP9, ABCG2, BMP2, CRMP1, IL2, IRF1, SOD2, IER3, NFKBIA, FN1, SERPINE1, MICA, TBP, CXCR2, BHMT, NCOR1, SNAI1, BAX, NPPB, CTSB, F8, IL12B, IGF2BP1, LCN2, NOLC1, CD40LG, SELE, NOD2, CCL5, FAS, ALOX5AP, OLR1, CXCR4, SDC1, FLT4, NCOR2, AKT2, CDH1, TGFB1, CCL3, IGF2BP2, HDAC1, SP1, PDE7A, ADORA3, CRHR1, BCL3, MIF, CXCL5, TNFRSF10B, HAX1, CYP27B1, NLRP2, FGF7, PTGER4, TNFRSF13C, CARM1, EBI3, VCAM1, ERAP2, MYC, CSF1, EPCAM, SLC25A27, NOS2, RIPK2, EGR1, BTG2, BCL2, ABCA1, CD69, BIRC2, CCR3, IL21, GCLC, MMP13, GRIN1, SP3, RRM2B, STAT4, TF, MUC6	2	COL1A2, COL1A1
RELA	NO	302	NRF1, OXTR, FTH1, CDK4, UPP1, IFNG, MMP2, DCST1, AGT, FLT4, EGFR, CCL4, NCAM1, VEGFA, CR2, CFI, TP53, FOXO3, CYP19A1, BGN, LPL, CXCL12, ELF3, PTHLH, IRF7, TNC, AGER, EDN1, SFTPA1, IGF2BP2, PPARA, SAA1, TSLP, GSK3A, IFNB1, GKN2, PLA2G2A, F3, IL10, KLK3, MMP12, IL17A, NR4A1, CEACAM1, AKT1, EPAS1, IL1RN, BAX, TRIB3, E2F1, PCK2, CXCL1, PTPN6, MMP3, CDK6, PIGR, ERAP1, YY1, OLFM4, IL18, LIPE, CD28, MMP9, TERT, IL4, NAMPT, BACE1, JUNB, CCR2, FASLG, ALOX5, BCL2L1, CCL11, PGR, GTF2B, CCL22, PLIN1, AKT2, BIRC3, HBEGF, CCL2, SERPINB1, MUC17, BAD, FGF7, PTGFR, TFF3, PTAFR, PTGS2, COX1, SERPINA3, ITGAX, CCND2, MCL1, TLR7, POU2F2, REPS2, TF, TFF1, SLC9A2, PLAU, TNF, FOXP3, HDAC7, MUC5B, NCOR1, FIGF, CYP3A4, SP1, CCL13, IFNA1, NOX5, MAT2A, COL7A1, HMOX1, ADORA1, TNFSF10, AR, CCR5, COL2A1, TAP1, IL1B, CD74, CD38, MUC5AC, GSTP1, MUC2, TIMP1, CCL19, CXCR4, FGF8, PDK4, CCL20, STK39, CYP3A7, GATA3, IRF4, CD58, HES1, PLAUR, SP4, NFKB1, MMP1, NOX4, BDKRB1, CASP3, CYP1A1, PTEN, HPSE, CCNB1, CD40, NOS3, ABCA1, PPARD, HIF1A, TNFRSF9, CD80, KDM2A, IL23A, TNFAIP3, TNFSF14, IL12A, TRPC1, CYP2E1, RGS4, ADORA2A, AMH, XIAP, MADCAM1, HYAL1, CFLAR, TBX21, ICAM1, BCL2L11, CHUK, TAP2, IL2RA, TLR3, ABCB1, IL17C, CCND1, KLF5, CCR7, CCK, DCST2, MMP14, FBP1, OPTN, IL1A, LTC4S, COL1A2, NOS1, WT1, BIRC5, PPIG, PTGES, THBD, CREB3, VWF, CXCL2, CRP, HLA-A, BCL2A1, BRCA2, IKBKB, GFAP, TWIST1, PSMB10, PROX1, COL1A1, TNIP3, NFKBIZ, TLR2, TNFRSF10A, S100A6, DRD2, CXCL8, BTG2, TRAF1, PTPN13, CD83, CSNK2A1, CARD8, CXCL10, CDKN1A, IL6, CFTR, CASP9, SIRT1, BMP2, IL2, IRF1, SOD2, IER3, NFKBIA, FN1, SERPINE1, MICA, TBP, CXCR2, BHMT, ABCG2, SNAI1, NOS2, PSMB9, CTSB, HSD11B2, F8, IL12B, IGF2BP1, LCN2, NOLC1, CD40LG, SELE, CCL5, FAS, ALOX5AP, OLR1, VCAM1, SDC1, SAA2, NCOR2, DEFB4A, CDH1, TRAF2, CCL3, GNRH2, HDAC1, TAPBP, CSF2, ADORA3, CRHR1, BCL3, MIF, CXCL5, TNFRSF10B, CYP27B1, NLRP2, FAF1, PTGER4, TNFRSF13C, CARM1, EBI3, ERAP2, CSF1, EPCAM, SLC25A27, RIPK2, EGR1, CD86, BCL2, CD69, BIRC2, CCR3, NPPB, GCLC, MMP13, GRIN1, SP3, MYC, STAT4, MUC6	2	COL1A2, COL1A1
MYB	NO	33	COL1A2, MYB, COL1A1, IL7, CEBPA, CTSG, GSTM1, IL15, SIM2, ERBB2, RAG2, TK1, WAS, CLEC4G, CDO1, LCK, DHRS2, CD34, GATA1, ICAM1, ANPEP, GATA3, BCL2, NR3C1, CD4, CCNA1, CSF3R, ELANE, SP3, NMU, MYC, MAT2A, PRTN3	2	COL1A2, COL1A1
STAT6	NO	38	BCL2L1, CCL11, CYP2E1, ORMDL3, ALOX15, ITGA2B, ADRA2B, EGLN3, FOS, IL13, PTGS2, SELE, EGR1, ALOX12, NCOA3, SOCS1, CYSLTR1, STAT1, SIDT1, CCL26, COL1A2, HSD3B2, FOSB, CNR1, CISH, SELP, OPRM1, CXCL8, CD40, DUSP1, IL24, FCER2, IRF4, IL1R1, CCL17, IL4, RHOA, COL1A1	2	COL1A2, COL1A1
SP1	NO	460	ITGB3, KRT14, CDK4, UGCG, PGR, GAST, PSIP1, ITGA5, PTHLH, ITGB2, CD44, HLA-G, LTF, IGFBP4, NF1, ACVRL1, GSTP1, CYP2F1, CA9, MMRN1, HSD17B2, STK11, FGFR3, CD28, UGT1A4, FASLG, DNASE2, KRT19, SLC39A1, ALOX5, PDGFB, PTGS2, CYP7A1, TNF, TPMT, HSD11B2, FMR1, CHI3L1, PCK1, DMRT1, RARA, RASSF1, CYP3A7, BRD7, CYP17A1, LPL, CXADR, PADI3, ABCA1, NR5A1, COL11A2, IRF5, XIAP, BACE1, STAR, TBX21, BSG, APP, MDM2, COMP, ALOX12, CHRNB4, SNAP25, MTA1, CCK, DDB2, CIC, ACAN, KIT, MAT2A, SERPINB5, CDH2, ICAM1, SLC29A1, USP7, SLC5A8, HTR1A, REST, IGF2, APOC3, APAF1, ABCG2, IFNGR1, CRMP1, SLC7A5, PDGFC, HNF4A, ATP2C1, MICA, EAPP, TNFRSF10B, KRT5, MACROD1, ERVW-1, CD151, ELF4, MMP28, POLD2, DNMT1, MAOB, CBS, E2F1, KCNQ3, COL18A1, HIST2H4A, RPS3A, IL10, C4A, CYP3A5, ST6GAL1, CD99, BCL2, SLC15A1, IL6, ADAM10, KRT16, POLE2, MUC6, CBFB, ACO1, DCK, CAV1, MIF, DNMT3A, HMGA2, PDIA2, B4GALT1, GJA1, PPL, SLC13A4, AGTR1, PTGIR, CETP, SLC2A2, CYP27A1, F2R, BLMH, ADIPOQ, CENPH, OPRM1, BAG2, MPO, WRN, CDK6, PTTG1, YY1, CD2AP, TBXA2R, TGM4, PRSS50, HSD17B11, HCN2, MYCN, F3, ID4, CDKN1A, SLC5A1, SERPINE1, C1QBP, SOX3, EGR1, TF, RETN, SYP, RORA, NDUFV1, C4B, SNAPC1, TGFBR2, MME, GATA3, DPYSL2, CXCL14, SPRY2, ABCB8, COX4I1, SCTR, UGDH, HBEGF, PLAT, FOS, XPC, MUC5AC, HYAL1, BRCA1, NOS1, KCTD11, HCN4, ASPN, OXTR, COL1A1, TLR2, ALOX15B, ITGAV, IL5, SLC9A2, SIRT1, FGL2, KLF8, KCNQ2, UGT2B15, FOXM1, TEC, CHST4, TINF2, SLC19A3, KIF2C, ADAM23, PTGES, DNMT3B, GCLC, THBD, GFER, ADRBK1, TGFB1, SLC25A20, TK1, PRM1, CXCL1, APOE, PDE6A, TICAM1, KCNH2, TERF2, CENPW, NFKB1, ITGA2, PCYT1A, SIGIRR, IRS2, SP3, GIPR, SCNN1B, PTN, PTEN, NDUFV2, INSR, AGT, ME1, ATP2A2, HAS2, CYP19A1, HTT, MAT2B, PRNP, MNDA, SLC9A3, ADAM17, BAX, SLC3A2, UTRN, SPN, PAX6, SMARCA1, IL2, CREM, MMP9, ENG, CHGA, MUC4, ESR1, AHR, ATM, NFKB2, COL7A1, CD97, EPO, TFPI2, POR, DRG2, ELMO3, CAT, CYP3A4, LOXL4, BDKRB1, WAS, PNOC, LDHC, ADH6, CDC42BPG, NKX2-1, CYP1B1, TAF7, PLAUR, MMP2, MMP11, APLNR, UBC, GM2A, FGFR1, PLAA, TIMP1, TNFSF14, PTK6, KISS1, CDKN2B, COL2A1, BTK, ITGAX, HBZ, CREB1, MMP14, MICB, LEP, FOLR1, ATP2A3, SNRPN, ADA, PSEN1, SPP1, TNNI3, NOL7, VEGFA, CSNK2A1, VAMP2, NQO2, LOR, EPOR, HSD3B1, ISG20, MET, F10, CD1D, FBLN1, APLP1, CCL5, FAS, ERBB2, COPS5, MYBL1, RECQL4, CD83, SOD1, HOXB7, WIF1, SLC39A8, CES1, IL5RA, APEX1, ITGAD, TNC, KDR, CLDN3, NR4A1, MYC, RELA, RECK, PGLYRP2, LRP5, MYBL2, ADRA2B, VIM, EGFR, GDA, SOD2, FES, LDHA, CD14, AMACR, IGFBP1, SLC19A1, IMPDH2, PDE6B, LCAT, PPP2R2B, FBN1, CERS2, EPAS1, KLK3, FLNA, CCL2, HMGA1, BACE2, EDNRB, FABP6, HPR, IGFBP3, PON1, APOA1, NPY, B4GALT5, FXR2, CCND2, STARD3, IL2RB, DDB1, SQSTM1, TERT, HGF, TNFSF10, KRT18, TYMP, MUC2, MPG, ABCC3, HDAC4, TCN2, TYMS, DBF4, CASP3, SGPL1, GH2, EGF, CCND1, GPR39, IVL, AR, NT5E, LYZ, SMPD1, PHGDH, CDKN2A, MGST1, CCNA2, POLD1, NOS3, ABCB1, DHCR24, LDLR, HSD17B1, SOCS1, FBP1, LTC4S, CTSL, BIRC5, HRAS, PDHA1, TIMP2, P4HA1, TMPO, ARF6, CDKN1B, SLC31A1, SOX9, PLAU, RGN, CTSB, EZR, TIMP3, F7, SREBF1, SKP2, SCT, VDR, ADRB3, CXCL5, LMO4, CD163, MCTS1, ATF2, CTGF, SRC, P2RX4, TGFA, IL3, CYP7B1, ADRA1A, GRIN1, SRY, ODC1	3	VDR, COL1A1, LRP5

regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
VDR	YES	17	WT1, SP1, STAT3, CDX2, TP63, TP73, KLF4, ZNF224, EZH2, PIAS4, JUN, SMAD3, POU1F1, SNAI1, SNW1, NCOA4, SNAI2	0
LRP5	YES	4	SP1, VDR, KLF15, RUNX2	1	VDR
COL1A2	YES	9	RFX5, STAT6, YY1, CEBPZ, MYB, RELA, CIITA, NFKB1, SIRT1	0
COL1A1	YES	12	SP1, RELA, NFKB1, MYBL2, TFAP2A, SP3, MYB, NFIC, MKL1, CIITA, STAT6, ETS1	0

Interactions from BIOGRID - physical

Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
VDR	COL1A1	No	1	BRCA1
LRP5	WNT1	No	1	FZD8
CALCR	COL1A1	No	1	THBS1
COL1A2	COL1A1	Yes	5	CAMKMT, ERAL1, PDGFA, PDGFB, COL1A1

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic

Interactions from STRING

Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
VDR	LRP5	No	-	1	SP7
VDR	WNT1	No	-	1	SMAD4
LRP5	CALCR	No	-	2	GCGR, PTH1R
LRP5	WNT1	Yes	activation, binding	28	WNT2B, SOST, WNT5A, FZD1, WNT8B, WNT8A, FZD2, WNT3A, WNT5B, AXIN1, FZD8, ROR2, WNT3, DKK1, DVL3, LRP6, WNT16, WNT7A, CSNK1G2, DVL1, GSK3B, FZD4, FZD10, WNT2, DVL2, BMP2, WNT7B, WNT4

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CORUM

Interactions from CENSUS

Interactions from PDB

Gene1	Gene2	Interaction	Number of common interactors	Common genes in interaction
COL1A2	COL1A1	Yes	5	COL9A2, COL9A3, COL1A2, COL9A1, COL1A1

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from manually curated literature

KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Platelet activation	hsa04611	5.66	2	COL1A2, COL1A1
Protein digestion and absorption	hsa04974	6.2	2	COL1A2, COL1A1
ECM-receptor interaction	hsa04512	6.09	2	COL1A2, COL1A1
Focal adhesion	hsa04510	4.92	2	COL1A2, COL1A1
Amoebiasis	hsa05146	5.82	2	COL1A2, COL1A1
Wnt signaling pathway	hsa04310	5.49	2	WNT1, LRP5
PI3K-Akt signaling pathway	hsa04151	4.21	2	COL1A2, COL1A1

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Cancers: Overview	NEW	2.72	0.036	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
Cancers: Specific types	NEW	4.1	0.004	VDR, COL1A1, WNT1, COL1A2, LRP5
Pathways in cancer (hsa05200)	NEW	3.98	0.008	VDR, COL1A1, WNT1, COL1A2, LRP5
Hippo signaling pathway (hsa04390)	NEW	5.37	0.003	LRP5, WNT1, COL1A1, COL1A2
Endocrine system	NEW	3.26	0.004	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
Cellular community	NEW	3.57	0.001	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
Wnt signaling pathway (hsa04310)	-	5.49	0.001	VDR, WNT1, COL1A2, LRP5

REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Signal Transduction	R-HSA-162582	1.78	3	LRP5, CALCR, WNT1
GPVI-mediated activation cascade	R-HSA-114604	7.18	2	COL1A2, COL1A1
Cell surface interactions at the vascular wall	R-HSA-202733	6.32	2	COL1A2, COL1A1
Extracellular matrix organization	R-HSA-1474244	4.91	2	COL1A2, COL1A1
disassembly of the destruction complex and recruitment of AXIN to the membrane	R-HSA-4641262	8.03	2	WNT1, LRP5
Integrin cell surface interactions	R-HSA-216083	6.57	2	COL1A2, COL1A1
Platelet activation, signaling and aggregation	R-HSA-76002	5.15	2	COL1A2, COL1A1
Anchoring fibril formation	R-HSA-2214320	9.08	2	COL1A2, COL1A1
Degradation of the extracellular matrix	R-HSA-1474228	6.11	2	COL1A2, COL1A1
ECM proteoglycans	R-HSA-3000178	6.75	2	COL1A2, COL1A1
Syndecan interactions	R-HSA-3000170	8.23	2	COL1A2, COL1A1
Non-integrin membrane-ECM interactions	R-HSA-3000171	7.1	2	COL1A2, COL1A1
Collagen biosynthesis and modifying enzymes	R-HSA-1650814	6.98	2	COL1A2, COL1A1
GPCR ligand binding	R-HSA-500792	4.19	2	WNT1, CALCR
TCF dependent signaling in response to WNT	R-HSA-201681	5.36	2	WNT1, LRP5
Platelet Adhesion to exposed collagen	R-HSA-75892	9.08	2	COL1A2, COL1A1
Vesicle-mediated transport	R-HSA-5653656	4.33	2	COL1A2, COL1A1
Class B/2 (Secretin family receptors)	R-HSA-373080	6.52	2	CALCR, WNT1
Binding and Uptake of Ligands by Scavenger Receptors	R-HSA-2173782	5.38	2	COL1A2, COL1A1
Signaling by Wnt	R-HSA-195721	4.79	2	WNT1, LRP5
Signaling by GPCR	R-HSA-372790	2.68	2	WNT1, CALCR
Collagen degradation	R-HSA-1442490	7.03	2	COL1A2, COL1A1
Crosslinking of collagen fibrils	R-HSA-2243919	9.52	2	COL1A2, COL1A1
Collagen formation	R-HSA-1474290	6.56	2	COL1A2, COL1A1
Scavenging by Class A Receptors	R-HSA-3000480	8.73	2	COL1A2, COL1A1
Assembly of collagen fibrils and other multimeric structures	R-HSA-2022090	7.2	2	COL1A2, COL1A1
Hemostasis	R-HSA-109582	3.98	2	COL1A2, COL1A1

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Class B/2 (Secretin family receptors) (R-HSA-373080)	-	6.52	0.0	LRP5, CALCR, WNT1, COL1A1
disassembly of the destruction complex and recruitment of AXIN to the membrane (R-HSA-4641262)	-	8.03	0.01	WNT1, LRP5
Signaling by GPCR (R-HSA-372790)	-	2.68	0.012	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
Scavenging by Class A Receptors (R-HSA-3000480)	-	8.73	0.02	COL1A2, COL1A1
beta-catenin independent WNT signaling (R-HSA-3858494)	NEW	5.83	0.034	LRP5, WNT1, COL1A1
Anchoring fibril formation (R-HSA-2214320)	-	9.08	0.002	COL1A2, COL1A1
WNT ligand biogenesis and trafficking (R-HSA-3238698)	NEW	8.28	0.026	WNT1, COL1A1
Crosslinking of collagen fibrils (R-HSA-2243919)	-	9.52	0.008	COL1A2, COL1A1
negative regulation of TCF-dependent signaling by WNT ligand antagonists (R-HSA-3772470)	NEW	9.08	0.004	WNT1, LRP5
Platelet Adhesion to exposed collagen (R-HSA-75892)	-	9.08	0.002	COL1A2, COL1A1
GPVI-mediated activation cascade (R-HSA-114604)	-	7.18	0.032	COL1A2, COL1A1
Syndecan interactions (R-HSA-3000170)	-	8.23	0.015	COL1A2, COL1A1
Non-integrin membrane-ECM interactions (R-HSA-3000171)	-	7.1	0.035	COL1A2, COL1A1
Collagen biosynthesis and modifying enzymes (R-HSA-1650814)	-	6.98	0.042	COL1A2, COL1A1
GPCR ligand binding (R-HSA-500792)	-	4.19	0.001	VDR, WNT1, COL1A1, LRP5, CALCR
Assembly of collagen fibrils and other multimeric structures (R-HSA-2022090)	-	7.2	0.031	COL1A2, COL1A1
Collagen degradation (R-HSA-1442490)	-	7.03	0.039	COL1A2, COL1A1

GO - molecular function annotation: shared terms / NET-GE enrichment

Shared terms

GO	IC	Number of genes with the same GO	Genes
binding (GO:0005488)	0.18	7	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
protein binding (GO:0005515)	0.46	7	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
cation binding (GO:0043169)	1.4	4	VDR, COL1A2, COL1A1, PDLIM4
metal ion binding (GO:0046872)	1.41	4	VDR, COL1A2, COL1A1, PDLIM4
signal transducer activity (GO:0004871)	2.28	4	VDR, WNT1, CALCR, LRP5
ion binding (GO:0043167)	1.36	4	VDR, COL1A2, COL1A1, PDLIM4
molecular transducer activity (GO:0060089)	2.32	3	VDR, CALCR, LRP5
signaling receptor activity (GO:0038023)	2.49	3	VDR, CALCR, LRP5
receptor activity (GO:0004872)	2.32	3	VDR, CALCR, LRP5
transcription regulatory region DNA binding (GO:0044212)	3.03	2	VDR, WNT1
extracellular matrix structural constituent (GO:0005201)	5.37	2	COL1A2, COL1A1
transition metal ion binding (GO:0046914)	2.48	2	VDR, PDLIM4
transporter activity (GO:0005215)	2.57	2	CALCR, LRP5
regulatory region DNA binding (GO:0000975)	3.03	2	VDR, WNT1
regulatory region nucleic acid binding (GO:0001067)	3.03	2	VDR, WNT1
growth factor binding (GO:0019838)	4.89	2	COL1A2, COL1A1
structural molecule activity (GO:0005198)	3.1	2	COL1A2, COL1A1
transmembrane signaling receptor activity (GO:0004888)	2.57	2	CALCR, LRP5
transmembrane receptor activity (GO:0099600)	2.53	2	CALCR, LRP5
nucleic acid binding (GO:0003676)	1.44	2	VDR, WNT1
DNA binding (GO:0003677)	1.92	2	VDR, WNT1
platelet-derived growth factor binding (GO:0048407)	7.34	2	COL1A2, COL1A1
receptor binding (GO:0005102)	2.43	2	VDR, WNT1
organic cyclic compound binding (GO:0097159)	1.05	2	VDR, WNT1
heterocyclic compound binding (GO:1901363)	1.06	2	VDR, WNT1
identical protein binding (GO:0042802)	2.63	2	COL1A2, COL1A1
zinc ion binding (GO:0008270)	2.66	2	VDR, PDLIM4

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
extracellular matrix structural constituent (GO:0005201)	-	5.37	0.026	COL1A2, COL1A1
signaling receptor activity (GO:0038023)	-	2.49	0.021	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
amide binding (GO:0033218)	NEW	4.14	0.01	VDR, CALCR, COL1A1, COL1A2
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	NEW	4.65	0.001	VDR, COL1A2, COL1A1, LRP5
growth factor binding (GO:0019838)	-	4.89	0.035	CALCR, COL1A1, COL1A2
vitamin binding (GO:0019842)	NEW	5.34	0.011	VDR, COL1A2, COL1A1
peptide binding (GO:0042277)	NEW	4.22	0.01	VDR, CALCR, COL1A1, COL1A2
transmembrane signaling receptor activity (GO:0004888)	-	2.57	0.01	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
G-protein coupled receptor binding (GO:0001664)	NEW	4.18	0.0	CALCR, WNT1, COL1A1, LRP5, COL1A2
platelet-derived growth factor binding (GO:0048407)	-	7.34	0.001	COL1A2, COL1A1
oxidoreductase activity (GO:0016491)	NEW	3.12	0.048	VDR, COL1A2, COL1A1, CALCR, LRP5

GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

GO	IC	Number of genes with the same GO	Genes
cellular process (GO:0009987)	0.26	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
cellular component organization (GO:0016043)	1.24	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
regulation of cellular process (GO:0050794)	0.5	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
organic substance metabolic process (GO:0071704)	0.63	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
single-organism cellular process (GO:0044763)	0.65	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
single-organism process (GO:0044699)	0.48	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
metabolic process (GO:0008152)	0.58	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
biological regulation (GO:0065007)	0.39	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
regulation of biological process (GO:0050789)	0.45	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
cellular component organization or biogenesis (GO:0071840)	1.22	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of metabolic process (GO:0009893)	1.74	5	VDR, WNT1, COL1A1, CALCR, LRP5
regulation of metabolic process (GO:0019222)	1.02	5	VDR, CALCR, WNT1, COL1A1, LRP5
positive regulation of biosynthetic process (GO:0009891)	2.29	5	VDR, WNT1, COL1A1, CALCR, LRP5
regulation of cellular biosynthetic process (GO:0031326)	1.38	5	VDR, WNT1, COL1A1, LRP5, CALCR
positive regulation of cellular metabolic process (GO:0031325)	1.81	5	VDR, CALCR, WNT1, COL1A1, LRP5
regulation of cellular metabolic process (GO:0031323)	1.07	5	VDR, CALCR, WNT1, COL1A1, LRP5
signal transduction (GO:0007165)	1.28	5	VDR, CALCR, WNT1, COL1A2, LRP5
anatomical structure morphogenesis (GO:0009653)	2.53	5	VDR, COL1A1, WNT1, COL1A2, LRP5
regulation of primary metabolic process (GO:0080090)	1.08	5	VDR, WNT1, COL1A1, LRP5, CALCR
cellular developmental process (GO:0048869)	1.82	5	VDR, CALCR, WNT1, COL1A1, LRP5
positive regulation of cellular biosynthetic process (GO:0031328)	2.3	5	VDR, CALCR, WNT1, COL1A1, LRP5
regulation of macromolecule metabolic process (GO:0060255)	1.08	5	VDR, CALCR, WNT1, COL1A1, LRP5
positive regulation of biological process (GO:0048518)	1.2	5	VDR, WNT1, COL1A1, LRP5, CALCR
negative regulation of biological process (GO:0048519)	1.33	5	VDR, COL1A1, WNT1, CALCR, LRP5
regulation of biological quality (GO:0065008)	1.68	5	VDR, CALCR, COL1A1, LRP5, COL1A2
regulation of gene expression (GO:0010468)	1.37	5	VDR, WNT1, COL1A1, CALCR, LRP5
developmental process (GO:0032502)	1.36	5	VDR, WNT1, COL1A1, LRP5, COL1A2
multicellular organismal process (GO:0032501)	1.45	5	VDR, COL1A1, WNT1, COL1A2, LRP5
positive regulation of nucleobase-containing compound metabolic process (GO:0045935)	2.35	5	VDR, COL1A1, WNT1, CALCR, LRP5
regulation of nucleobase-containing compound metabolic process (GO:0019219)	1.43	5	VDR, WNT1, COL1A1, LRP5, CALCR
regulation of biosynthetic process (GO:0009889)	1.37	5	VDR, COL1A1, WNT1, CALCR, LRP5
single-organism developmental process (GO:0044767)	1.49	5	VDR, WNT1, COL1A1, COL1A2, LRP5
regulation of nitrogen compound metabolic process (GO:0051171)	1.36	5	VDR, COL1A1, WNT1, CALCR, LRP5
regulation of multicellular organismal process (GO:0051239)	1.87	5	VDR, COL1A1, WNT1, CALCR, LRP5
positive regulation of nitrogen compound metabolic process (GO:0051173)	2.29	5	VDR, CALCR, WNT1, COL1A1, LRP5
single-multicellular organism process (GO:0044707)	1.78	5	VDR, COL1A1, WNT1, COL1A2, LRP5
anatomical structure development (GO:0048856)	1.58	5	VDR, WNT1, COL1A1, LRP5, COL1A2
macromolecule metabolic process (GO:0043170)	0.83	5	VDR, CALCR, WNT1, COL1A1, COL1A2
positive regulation of cellular process (GO:0048522)	1.3	5	VDR, WNT1, COL1A1, LRP5, CALCR
macromolecular complex subunit organization (GO:0043933)	2.14	4	LRP5, WNT1, COL1A1, COL1A2
regulation of response to stimulus (GO:0048583)	1.54	4	WNT1, COL1A1, LRP5, COL1A2
positive regulation of gene expression (GO:0010628)	2.35	4	VDR, COL1A1, WNT1, LRP5
cell surface receptor signaling pathway (GO:0007166)	2.09	4	CALCR, WNT1, COL1A2, LRP5
response to endogenous stimulus (GO:0009719)	2.79	4	CALCR, WNT1, COL1A1, COL1A2
single-organism metabolic process (GO:0044710)	1.63	4	CALCR, COL1A1, LRP5, COL1A2
positive regulation of macromolecule metabolic process (GO:0010604)	1.81	4	VDR, COL1A1, WNT1, LRP5
protein complex subunit organization (GO:0071822)	2.6	4	LRP5, WNT1, COL1A1, COL1A2
regulation of cellular macromolecule biosynthetic process (GO:2000112)	1.46	4	VDR, COL1A1, WNT1, LRP5
localization (GO:0051179)	1.4	4	VDR, COL1A1, CALCR, LRP5
positive regulation of molecular function (GO:0044093)	2.23	4	VDR, WNT1, CALCR, LRP5
regulation of molecular function (GO:0065009)	1.78	4	VDR, CALCR, WNT1, LRP5
positive regulation of nucleic acid-templated transcription (GO:1903508)	2.56	4	VDR, WNT1, COL1A1, LRP5
organ morphogenesis (GO:0009887)	3.55	4	VDR, COL1A1, COL1A2, LRP5
transport (GO:0006810)	1.51	4	VDR, COL1A1, CALCR, LRP5
regulation of nucleic acid-templated transcription (GO:1903506)	1.55	4	VDR, WNT1, COL1A1, LRP5
regulation of cell differentiation (GO:0045595)	2.42	4	VDR, WNT1, COL1A1, LRP5
positive regulation of transcription, DNA-templated (GO:0045893)	2.56	4	VDR, WNT1, COL1A1, LRP5
regulation of RNA biosynthetic process (GO:2001141)	1.55	4	VDR, WNT1, COL1A1, LRP5
response to chemical (GO:0042221)	1.98	4	CALCR, WNT1, COL1A1, COL1A2
establishment of localization (GO:0051234)	1.48	4	VDR, COL1A1, CALCR, LRP5
catabolic process (GO:0009056)	2.38	4	WNT1, COL1A1, LRP5, COL1A2
response to organic substance (GO:0010033)	2.2	4	CALCR, WNT1, COL1A1, COL1A2
response to stimulus (GO:0050896)	1.22	4	CALCR, WNT1, COL1A1, COL1A2
regulation of RNA metabolic process (GO:0051252)	1.52	4	VDR, WNT1, COL1A1, LRP5
positive regulation of RNA metabolic process (GO:0051254)	2.51	4	VDR, WNT1, COL1A1, LRP5
positive regulation of RNA biosynthetic process (GO:1902680)	2.54	4	VDR, COL1A1, WNT1, LRP5
regulation of transcription, DNA-templated (GO:0006355)	1.56	4	VDR, COL1A1, WNT1, LRP5
positive regulation of macromolecule biosynthetic process (GO:0010557)	2.39	4	VDR, WNT1, COL1A1, LRP5
regulation of macromolecule biosynthetic process (GO:0010556)	1.43	4	VDR, COL1A1, WNT1, LRP5
system development (GO:0048731)	2.92	4	VDR, COL1A2, COL1A1, LRP5
negative regulation of cellular process (GO:0048523)	1.41	4	VDR, WNT1, COL1A1, LRP5
cellular response to endogenous stimulus (GO:0071495)	3.33	3	WNT1, COL1A1, COL1A2
negative regulation of metabolic process (GO:0009892)	1.93	3	VDR, WNT1, LRP5
regulation of anatomical structure morphogenesis (GO:0022603)	2.79	3	VDR, WNT1, COL1A1
cell differentiation (GO:0030154)	2.14	3	CALCR, COL1A1, WNT1
branching morphogenesis of an epithelial tube (GO:0048754)	4.93	3	VDR, WNT1, LRP5
regulation of cellular component organization (GO:0051128)	2.01	3	LRP5, WNT1, COL1A1
homeostatic process (GO:0042592)	2.61	3	VDR, CALCR, LRP5
skeletal system development (GO:0001501)	4.49	3	VDR, COL1A2, COL1A1
regulation of Wnt signaling pathway (GO:0030111)	3.98	3	LRP5, WNT1, COL1A1
positive regulation of developmental process (GO:0051094)	2.77	3	VDR, WNT1, COL1A1
morphogenesis of a branching structure (GO:0001763)	4.71	3	VDR, WNT1, LRP5
cellular response to chemical stimulus (GO:0070887)	2.57	3	WNT1, COL1A1, COL1A2
regulation of signaling (GO:0023051)	1.72	3	WNT1, COL1A1, LRP5
regulation of phosphate metabolic process (GO:0019220)	2.35	3	LRP5, CALCR, WNT1
regulation of cell communication (GO:0010646)	1.73	3	WNT1, COL1A1, LRP5
multicellular organism development (GO:0007275)	2.54	3	VDR, WNT1, LRP5
single-organism catabolic process (GO:0044712)	3.21	3	LRP5, COL1A1, COL1A2
morphogenesis of an epithelium (GO:0002009)	4.08	3	VDR, WNT1, LRP5
cellular response to stimulus (GO:0051716)	1.97	3	WNT1, COL1A1, COL1A2
negative regulation of macromolecule metabolic process (GO:0010605)	2.01	3	VDR, WNT1, LRP5
cellular macromolecule metabolic process (GO:0044260)	0.93	3	VDR, CALCR, WNT1
regulation of signal transduction (GO:0009966)	1.84	3	WNT1, COL1A1, LRP5
positive regulation of multicellular organismal process (GO:0051240)	2.49	3	VDR, WNT1, COL1A1
morphogenesis of a branching epithelium (GO:0061138)	4.77	3	VDR, WNT1, LRP5
cellular response to organic substance (GO:0071310)	2.78	3	WNT1, COL1A1, COL1A2
animal organ development (GO:0048513)	2.53	3	WNT1, COL1A1, LRP5
tissue morphogenesis (GO:0048729)	3.87	3	VDR, WNT1, LRP5
positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	2.81	3	VDR, WNT1, LRP5
cell migration (GO:0016477)	3.12	3	LRP5, COL1A1, COL1A2
regulation of cell proliferation (GO:0042127)	2.41	3	VDR, WNT1, LRP5
locomotion (GO:0040011)	2.91	3	LRP5, COL1A1, COL1A2
negative regulation of cellular metabolic process (GO:0031324)	2.01	3	VDR, WNT1, LRP5
tube morphogenesis (GO:0035239)	4.35	3	VDR, WNT1, LRP5
regulation of body fluid levels (GO:0050878)	3.76	3	VDR, COL1A2, COL1A1
primary metabolic process (GO:0044238)	0.69	3	VDR, WNT1, LRP5
regulation of developmental process (GO:0050793)	2.1	3	VDR, WNT1, COL1A1
regulation of catalytic activity (GO:0050790)	1.97	3	VDR, CALCR, LRP5
tissue development (GO:0009888)	3.27	3	VDR, LRP5, COL1A1
regulation of phosphorus metabolic process (GO:0051174)	2.35	3	LRP5, WNT1, CALCR
cell activation (GO:0001775)	3.47	3	WNT1, COL1A1, COL1A2
cell communication (GO:0007154)	3.04	3	WNT1, COL1A1, LRP5
movement of cell or subcellular component (GO:0006928)	2.61	3	LRP5, COL1A1, COL1A2
response to oxygen-containing compound (GO:1901700)	2.57	3	WNT1, COL1A1, COL1A2
cellular response to oxygen-containing compound (GO:1901701)	3.22	3	WNT1, COL1A1, COL1A2
cell motility (GO:0048870)	3.02	3	LRP5, COL1A1, COL1A2
response to hormone (GO:0009725)	3.33	3	WNT1, COL1A1, CALCR
response to organonitrogen compound (GO:0010243)	3.2	3	WNT1, COL1A1, COL1A2
cellular response to nitrogen compound (GO:1901699)	3.79	3	WNT1, COL1A1, COL1A2
positive regulation of cell differentiation (GO:0045597)	3.01	3	VDR, LRP5, COL1A1
cellular metabolic process (GO:0044237)	0.69	3	VDR, WNT1, CALCR
chemical homeostasis (GO:0048878)	2.97	3	VDR, CALCR, LRP5
immune system process (GO:0002376)	2.29	3	WNT1, COL1A1, COL1A2
regulation of transcription from RNA polymerase II promoter (GO:0006357)	2.24	3	VDR, WNT1, LRP5
regulation of multicellular organismal development (GO:2000026)	2.31	3	VDR, WNT1, COL1A1
cellular response to organonitrogen compound (GO:0071417)	3.87	3	WNT1, COL1A1, COL1A2
positive regulation of cellular component organization (GO:0051130)	2.68	3	WNT1, COL1A1, LRP5
response to nitrogen compound (GO:1901698)	3.12	3	WNT1, COL1A1, COL1A2
regulation of canonical Wnt signaling pathway (GO:0060828)	4.26	3	LRP5, WNT1, COL1A1
protein localization (GO:0008104)	2.36	2	CALCR, COL1A1
hemostasis (GO:0007599)	4.5	2	COL1A2, COL1A1
cellular cation homeostasis (GO:0030003)	3.6	2	VDR, CALCR
blood coagulation (GO:0007596)	4.52	2	COL1A2, COL1A1
cell development (GO:0048468)	3.28	2	WNT1, LRP5
negative regulation of cell adhesion (GO:0007162)	4.33	2	WNT1, COL1A1
calcium ion homeostasis (GO:0055074)	3.97	2	VDR, CALCR
inorganic ion homeostasis (GO:0098771)	3.43	2	VDR, CALCR
cell surface receptor signaling pathway involved in cell-cell signaling (GO:1905114)	3.79	2	WNT1, LRP5
organic cyclic compound metabolic process (GO:1901360)	1.26	2	VDR, LRP5
response to amino acid (GO:0043200)	5.12	2	COL1A2, COL1A1
regulation of localization (GO:0032879)	1.94	2	LRP5, COL1A1
cellular macromolecule localization (GO:0070727)	3.1	2	CALCR, COL1A1
positive regulation of signal transduction (GO:0009967)	2.5	2	WNT1, COL1A1
response to wounding (GO:0009611)	4.39	2	WNT1, COL1A1
regulation of cellular protein metabolic process (GO:0032268)	1.99	2	WNT1, LRP5
macromolecule localization (GO:0033036)	2.34	2	CALCR, COL1A1
ion homeostasis (GO:0050801)	3.42	2	VDR, CALCR
cellular homeostasis (GO:0019725)	3.23	2	VDR, CALCR
positive regulation of response to stimulus (GO:0048584)	2.18	2	WNT1, COL1A1
response to corticosteroid (GO:0031960)	4.56	2	CALCR, COL1A1
organic substance transport (GO:0071702)	2.15	2	CALCR, COL1A1
protein heterooligomerization (GO:0051291)	5.22	2	COL1A2, COL1A1
positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	4.29	2	WNT1, LRP5
establishment of protein localization (GO:0045184)	2.53	2	CALCR, COL1A1
regulation of immune response (GO:0050776)	2.98	2	COL1A2, COL1A1
regionalization (GO:0003002)	4.24	2	WNT1, LRP5
response to peptide hormone (GO:0043434)	4.06	2	WNT1, COL1A1
platelet activation (GO:0030168)	4.96	2	COL1A2, COL1A1
system process (GO:0003008)	2.3	2	VDR, COL1A1
regulation of phosphorylation (GO:0042325)	2.5	2	WNT1, LRP5
single organism signaling (GO:0044700)	3.25	2	WNT1, LRP5
vesicle-mediated transport (GO:0016192)	2.72	2	CALCR, LRP5
Wnt signaling pathway (GO:0016055)	3.88	2	WNT1, LRP5
collagen fibril organization (GO:0030199)	6.07	2	COL1A2, COL1A1
extracellular matrix organization (GO:0030198)	4.01	2	COL1A2, COL1A1
cellular component assembly (GO:0022607)	2.14	2	COL1A2, COL1A1
positive regulation of canonical Wnt signaling pathway (GO:0090263)	4.95	2	WNT1, COL1A1
positive regulation of Wnt signaling pathway (GO:0030177)	4.7	2	WNT1, COL1A1
intracellular signal transduction (GO:0035556)	2.39	2	WNT1, COL1A2
regulation of apoptotic process (GO:0042981)	2.5	2	VDR, LRP5
organic substance biosynthetic process (GO:1901576)	1.34	2	VDR, COL1A1
organic substance catabolic process (GO:1901575)	2.45	2	WNT1, LRP5
blood vessel development (GO:0001568)	4.95	2	COL1A2, COL1A1
macromolecular complex assembly (GO:0065003)	2.55	2	COL1A2, COL1A1
regulation of immune system process (GO:0002682)	2.5	2	COL1A2, COL1A1
positive regulation of catalytic activity (GO:0043085)	2.4	2	VDR, CALCR
anatomical structure formation involved in morphogenesis (GO:0048646)	3.01	2	WNT1, COL1A1
beta-catenin destruction complex disassembly (GO:1904886)	6.64	2	WNT1, LRP5
protein complex assembly (GO:0006461)	2.78	2	COL1A2, COL1A1
protein trimerization (GO:0070206)	6.04	2	COL1A2, COL1A1
protein heterotrimerization (GO:0070208)	7.09	2	COL1A2, COL1A1
canonical Wnt signaling pathway (GO:0060070)	5.26	2	WNT1, LRP5
response to stress (GO:0006950)	1.8	2	WNT1, COL1A1
coagulation (GO:0050817)	4.51	2	COL1A2, COL1A1
regulation of ossification (GO:0030278)	4.53	2	CALCR, LRP5
negative regulation of ossification (GO:0030279)	5.48	2	CALCR, LRP5
leukocyte differentiation (GO:0002521)	4.13	2	CALCR, WNT1
endocytosis (GO:0006897)	3.69	2	CALCR, LRP5
anterior/posterior pattern specification (GO:0009952)	4.71	2	WNT1, LRP5
negative regulation of protein modification process (GO:0031400)	3.4	2	WNT1, LRP5
collagen catabolic process (GO:0030574)	5.57	2	COL1A2, COL1A1
regulation of cell adhesion (GO:0030155)	3.27	2	WNT1, COL1A1
positive regulation of signaling (GO:0023056)	2.41	2	WNT1, COL1A1
cell adhesion (GO:0007155)	2.82	2	WNT1, COL1A1
signaling (GO:0023052)	3.25	2	WNT1, LRP5
collagen metabolic process (GO:0032963)	5.42	2	COL1A2, COL1A1
positive regulation of cell communication (GO:0010647)	2.41	2	WNT1, COL1A1
multicellular organism catabolic process (GO:0044243)	5.47	2	COL1A2, COL1A1
protein complex disassembly (GO:0043241)	4.58	2	WNT1, LRP5
response to organic cyclic compound (GO:0014070)	3.07	2	CALCR, COL1A1
divalent inorganic cation homeostasis (GO:0072507)	3.9	2	VDR, CALCR
negative regulation of protein metabolic process (GO:0051248)	2.82	2	WNT1, LRP5
cellular divalent inorganic cation homeostasis (GO:0072503)	3.96	2	VDR, CALCR
positive regulation of phosphorus metabolic process (GO:0010562)	2.78	2	CALCR, WNT1
negative regulation of multicellular organismal process (GO:0051241)	2.84	2	CALCR, LRP5
regulation of protein metabolic process (GO:0051246)	1.93	2	WNT1, LRP5
branching involved in mammary gland duct morphogenesis (GO:0060444)	6.78	2	VDR, LRP5
regulation of protein modification process (GO:0031399)	2.32	2	WNT1, LRP5
biological adhesion (GO:0022610)	2.81	2	WNT1, COL1A1
positive regulation of cell proliferation (GO:0008284)	3.01	2	WNT1, LRP5
cellular metal ion homeostasis (GO:0006875)	3.75	2	VDR, CALCR
cellular calcium ion homeostasis (GO:0006874)	4.01	2	VDR, CALCR
cellular ion homeostasis (GO:0006873)	3.57	2	VDR, CALCR
biosynthetic process (GO:0009058)	1.32	2	VDR, COL1A1
negative regulation of cell differentiation (GO:0045596)	3.33	2	WNT1, LRP5
response to acid chemical (GO:0001101)	4.05	2	COL1A2, COL1A1
multicellular organismal macromolecule metabolic process (GO:0044259)	5.36	2	COL1A2, COL1A1
cation homeostasis (GO:0055080)	3.46	2	VDR, CALCR
cellular chemical homeostasis (GO:0055082)	3.4	2	VDR, CALCR
cellular response to acid chemical (GO:0071229)	4.67	2	COL1A2, COL1A1
regulation of fat cell differentiation (GO:0045598)	5.04	2	WNT1, LRP5
protein oligomerization (GO:0051259)	3.71	2	COL1A2, COL1A1
negative regulation of cellular protein metabolic process (GO:0032269)	2.88	2	WNT1, LRP5
regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	3.83	2	WNT1, LRP5
response to steroid hormone (GO:0048545)	4.24	2	CALCR, COL1A1
bone development (GO:0060348)	5.82	2	WNT1, LRP5
leukocyte migration (GO:0050900)	4.19	2	COL1A2, COL1A1
regulation of blood pressure (GO:0008217)	4.72	2	COL1A2, LRP5
regulation of cell death (GO:0010941)	2.43	2	VDR, LRP5
pattern specification process (GO:0007389)	3.79	2	WNT1, LRP5
macromolecular complex disassembly (GO:0032984)	4.53	2	WNT1, LRP5
response to lipid (GO:0033993)	3.11	2	CALCR, COL1A1
regulation of programmed cell death (GO:0043067)	2.49	2	VDR, LRP5
extracellular structure organization (GO:0043062)	4.0	2	COL1A2, COL1A1
skin morphogenesis (GO:0043589)	7.53	2	COL1A2, COL1A1
embryonic morphogenesis (GO:0048598)	3.72	2	WNT1, LRP5
regulation of tissue remodeling (GO:0034103)	5.55	2	VDR, LRP5
cellular response to amino acid stimulus (GO:0071230)	5.7	2	COL1A2, COL1A1
positive regulation of phosphate metabolic process (GO:0045937)	2.78	2	WNT1, CALCR
regulation of cell-substrate adhesion (GO:0010810)	4.56	2	WNT1, COL1A1
negative regulation of cell-substrate adhesion (GO:0010812)	5.76	2	WNT1, COL1A1
cellular protein localization (GO:0034613)	3.11	2	CALCR, COL1A1
single-organism transport (GO:0044765)	2.18	2	VDR, CALCR
macromolecule biosynthetic process (GO:0009059)	1.61	2	VDR, COL1A1
cellular component disassembly (GO:0022411)	3.52	2	WNT1, LRP5
metal ion homeostasis (GO:0055065)	3.61	2	VDR, CALCR
cell-cell signaling (GO:0007267)	3.35	2	WNT1, LRP5
single-organism localization (GO:1902578)	2.09	2	VDR, CALCR
cellular localization (GO:0051641)	2.32	2	CALCR, COL1A1
multicellular organism metabolic process (GO:0044236)	5.2	2	COL1A2, COL1A1
response to peptide (GO:1901652)	3.94	2	WNT1, COL1A1
regulation of organ morphogenesis (GO:2000027)	4.22	2	VDR, WNT1
protein transport (GO:0015031)	2.62	2	CALCR, COL1A1
regulation of protein phosphorylation (GO:0001932)	2.57	2	WNT1, LRP5

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
response to nitrogen compound (GO:1901698)	-	3.12	0.024	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
limb morphogenesis (GO:0035108)	NEW	5.05	0.003	VDR, WNT1, COL1A1, LRP5
embryonic limb morphogenesis (GO:0030326)	NEW	5.24	0.001	VDR, WNT1, COL1A1, LRP5
regulation of anatomical structure morphogenesis (GO:0022603)	-	2.79	0.001	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
regeneration (GO:0031099)	NEW	4.7	0.004	VDR, WNT1, COL1A1, LRP5
embryonic appendage morphogenesis (GO:0035113)	NEW	5.24	0.001	VDR, WNT1, COL1A1, LRP5
appendage morphogenesis (GO:0035107)	NEW	5.05	0.003	VDR, WNT1, COL1A1, LRP5
negative regulation of cell proliferation (GO:0008285)	NEW	3.26	0.018	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
branching morphogenesis of an epithelial tube (GO:0048754)	-	4.93	0.014	VDR, COL1A1, WNT1, LRP5
cellular response to acid chemical (GO:0071229)	-	4.67	0.025	CALCR, WNT1, COL1A1, COL1A2
skeletal system development (GO:0001501)	-	4.49	0.009	VDR, WNT1, COL1A1, COL1A2, CALCR
morphogenesis of a branching structure (GO:0001763)	-	4.71	0.01	VDR, WNT1, COL1A1, COL1A2, LRP5
positive regulation of intracellular signal transduction (GO:1902533)	NEW	2.95	0.022	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of nucleobase-containing compound metabolic process (GO:0045935)	-	2.35	0.009	VDR, WNT1, COL1A1, LRP5, CALCR
anatomical structure morphogenesis (GO:0009653)	-	2.53	0.006	VDR, COL1A1, WNT1, COL1A2, LRP5
negative regulation of catalytic activity (GO:0043086)	NEW	3.0	0.041	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
regulation of MAPK cascade (GO:0043408)	NEW	3.22	0.004	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
response to endogenous stimulus (GO:0009719)	-	2.79	0.0	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
morphogenesis of an epithelium (GO:0002009)	-	4.08	0.011	VDR, COL1A1, WNT1, COL1A2, LRP5
negative regulation of hydrolase activity (GO:0051346)	NEW	3.74	0.031	VDR, CALCR, WNT1, COL1A1, COL1A2
developmental process involved in reproduction (GO:0003006)	NEW	3.36	0.015	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of signal transduction (GO:0009967)	-	2.5	0.007	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
positive regulation of phosphorus metabolic process (GO:0010562)	-	2.78	0.002	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
positive regulation of cellular biosynthetic process (GO:0031328)	-	2.3	0.012	VDR, COL1A1, WNT1, CALCR, LRP5
gonad development (GO:0008406)	NEW	4.92	0.007	CALCR, COL1A1, LRP5, COL1A2
response to wounding (GO:0009611)	-	4.39	0.035	LRP5, WNT1, COL1A1, COL1A2
response to mechanical stimulus (GO:0009612)	NEW	4.41	0.037	VDR, CALCR, COL1A1, COL1A2
regulation of anatomical structure size (GO:0090066)	NEW	3.78	0.002	VDR, WNT1, COL1A2, CALCR, LRP5
negative regulation of peptidase activity (GO:0010466)	NEW	4.22	0.003	CALCR, WNT1, COL1A1, COL1A2, LRP5
positive regulation of cellular protein metabolic process (GO:0032270)	NEW	2.49	0.004	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
tissue morphogenesis (GO:0048729)	-	3.87	0.025	VDR, WNT1, COL1A1, COL1A2, LRP5
regulation of alcohol biosynthetic process (GO:1902930)	NEW	6.2	0.014	VDR, CALCR, LRP5
branching involved in mammary gland duct morphogenesis (GO:0060444)	-	6.78	0.014	VDR, LRP5
negative regulation of cell-substrate adhesion (GO:0010812)	-	5.76	0.014	WNT1, COL1A1, COL1A2
skin morphogenesis (GO:0043589)	-	7.53	0.026	COL1A2, COL1A1
cellular response to endogenous stimulus (GO:0071495)	-	3.33	0.044	VDR, WNT1, COL1A1, COL1A2
response to oxygen-containing compound (GO:1901700)	-	2.57	0.004	VDR, WNT1, COL1A1, COL1A2, LRP5
organ morphogenesis (GO:0009887)	-	3.55	0.002	VDR, COL1A2, COL1A1, LRP5
reproductive structure development (GO:0048608)	NEW	4.08	0.009	VDR, CALCR, COL1A1, COL1A2, LRP5
protein trimerization (GO:0070206)	-	6.04	0.036	COL1A2, COL1A1
positive regulation of phosphate metabolic process (GO:0045937)	-	2.78	0.002	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
morphogenesis of a branching epithelium (GO:0061138)	-	4.77	0.024	VDR, COL1A1, WNT1, LRP5
positive regulation of protein metabolic process (GO:0051247)	NEW	2.43	0.006	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
negative regulation of cell death (GO:0060548)	NEW	2.95	0.031	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
eye morphogenesis (GO:0048592)	NEW	5.9	0.012	LRP5, COL1A1, COL1A2
protein heterotrimerization (GO:0070208)	-	7.09	0.004	COL1A2, COL1A1
positive regulation of cell differentiation (GO:0045597)	-	3.01	0.024	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
pattern specification process (GO:0007389)	-	3.79	0.045	VDR, WNT1, COL1A1, COL1A2, LRP5
regulation of cartilage development (GO:0061035)	NEW	5.6	0.025	VDR, WNT1, COL1A1
regulation of steroid biosynthetic process (GO:0050810)	NEW	5.84	0.032	VDR, CALCR, LRP5
response to acid chemical (GO:0001101)	-	4.05	0.0	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of nitrogen compound metabolic process (GO:0051173)	-	2.29	0.01	VDR, CALCR, WNT1, COL1A1, LRP5
negative regulation of endopeptidase activity (GO:0010951)	NEW	4.26	0.002	CALCR, WNT1, COL1A1, COL1A2, LRP5
response to chemical (GO:0042221)	-	1.98	0.019	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
regulation of ossification (GO:0030278)	-	4.53	0.038	VDR, COL1A2, LRP5, PDLIM4
bone development (GO:0060348)	-	5.82	0.0	LRP5, WNT1, COL1A1, COL1A2
positive regulation of biosynthetic process (GO:0009891)	-	2.29	0.013	VDR, WNT1, COL1A1, LRP5, CALCR
response to organic substance (GO:0010033)	-	2.2	0.002	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
negative regulation of developmental process (GO:0051093)	NEW	3.17	0.037	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
cellular response to oxygen-containing compound (GO:1901701)	-	3.22	0.026	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of phosphorylation (GO:0042327)	NEW	2.9	0.001	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
aging (GO:0007568)	NEW	4.16	0.002	VDR, COL1A1, CALCR, COL1A2, LRP5
anterior/posterior pattern specification (GO:0009952)	-	4.71	0.024	VDR, COL1A1, WNT1, LRP5
positive regulation of developmental process (GO:0051094)	-	2.77	0.038	VDR, WNT1, COL1A1, LRP5
response to hormone (GO:0009725)	-	3.33	0.001	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
response to organonitrogen compound (GO:0010243)	-	3.2	0.018	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
positive regulation of protein modification process (GO:0031401)	NEW	2.7	0.002	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
regulation of cellular component biogenesis (GO:0044087)	NEW	3.08	0.004	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
collagen fibril organization (GO:0030199)	-	6.07	0.049	COL1A2, COL1A1
response to estrogen (GO:0043627)	NEW	5.25	0.031	VDR, CALCR, COL1A1, COL1A2
response to lipid (GO:0033993)	-	3.11	0.024	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
system development (GO:0048731)	-	2.92	0.05	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
regulation of protein phosphorylation (GO:0001932)	-	2.57	0.004	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
positive regulation of protein phosphorylation (GO:0001934)	NEW	2.95	0.0	VDR, LRP5, WNT1, CALCR, COL1A1, COL1A2, PDLIM4
response to steroid hormone (GO:0048545)	-	4.24	0.038	VDR, COL1A1, CALCR, COL1A2, LRP5
regionalization (GO:0003002)	-	4.24	0.006	VDR, WNT1, COL1A1, COL1A2, LRP5

GO - cellular component annotation: shared terms / NET-GE enrichment

Shared terms

GO	IC	Number of genes with the same GO	Genes
intracellular part (GO:0044424)	0.28	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
cell part (GO:0044464)	0.11	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
membrane-bounded organelle (GO:0043227)	0.47	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
organelle (GO:0043226)	0.4	6	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
cytoplasmic part (GO:0044444)	0.82	5	LRP5, CALCR, WNT1, COL1A1, COL1A2
protein complex (GO:0043234)	1.51	4	VDR, COL1A1, COL1A2, LRP5
macromolecular complex (GO:0032991)	1.35	4	VDR, COL1A1, COL1A2, LRP5
vesicle (GO:0031982)	1.64	4	CALCR, WNT1, COL1A1, COL1A2
membrane (GO:0016020)	0.68	4	CALCR, WNT1, COL1A1, LRP5
membrane-bounded vesicle (GO:0031988)	1.71	4	CALCR, WNT1, COL1A1, COL1A2
intracellular organelle part (GO:0044446)	0.81	4	VDR, WNT1, COL1A1, COL1A2
intracellular organelle (GO:0043229)	0.51	4	VDR, COL1A1, CALCR, LRP5
organelle part (GO:0044422)	0.79	4	VDR, WNT1, COL1A1, COL1A2
intracellular membrane-bounded organelle (GO:0043231)	0.6	4	VDR, CALCR, COL1A1, LRP5
extracellular space (GO:0005615)	2.63	3	WNT1, COL1A1, COL1A2
intracellular organelle lumen (GO:0070013)	3.05	3	WNT1, COL1A1, COL1A2
extracellular region part (GO:0044421)	1.57	3	WNT1, COL1A1, COL1A2
integral component of membrane (GO:0016021)	1.14	3	CALCR, COL1A1, LRP5
organelle lumen (GO:0043233)	3.05	3	WNT1, COL1A1, COL1A2
endoplasmic reticulum lumen (GO:0005788)	4.5	3	WNT1, COL1A1, COL1A2
extracellular matrix (GO:0031012)	3.81	3	WNT1, COL1A1, COL1A2
endoplasmic reticulum part (GO:0044432)	2.73	3	WNT1, COL1A1, COL1A2
extracellular region (GO:0005576)	2.18	3	WNT1, COL1A1, COL1A2
membrane-enclosed lumen (GO:0031974)	3.05	3	WNT1, COL1A1, COL1A2
plasma membrane (GO:0005886)	1.39	3	LRP5, WNT1, CALCR
membrane part (GO:0044425)	0.95	3	CALCR, COL1A1, LRP5
proteinaceous extracellular matrix (GO:0005578)	4.01	3	WNT1, COL1A1, COL1A2
intrinsic component of membrane (GO:0031224)	1.13	3	LRP5, CALCR, COL1A1
cytoplasm (GO:0005737)	1.01	2	WNT1, COL1A1
collagen type I trimer (GO:0005584)	9.11	2	COL1A2, COL1A1
extracellular organelle (GO:0043230)	1.89	2	WNT1, COL1A2
endoplasmic reticulum (GO:0005783)	2.56	2	COL1A1, LRP5
secretory vesicle (GO:0099503)	4.0	2	CALCR, COL1A1
fibrillar collagen trimer (GO:0005583)	7.32	2	COL1A2, COL1A1
cytoplasmic, membrane-bounded vesicle (GO:0016023)	3.12	2	CALCR, COL1A1
secretory granule (GO:0030141)	4.34	2	CALCR, COL1A1
cytoplasmic vesicle (GO:0031410)	2.87	2	CALCR, COL1A1
extracellular matrix component (GO:0044420)	4.97	2	COL1A2, COL1A1
intracellular vesicle (GO:0097708)	2.86	2	CALCR, COL1A1
collagen trimer (GO:0005581)	5.21	2	COL1A2, COL1A1
receptor complex (GO:0043235)	4.01	2	VDR, LRP5
extracellular vesicle (GO:1903561)	1.89	2	WNT1, COL1A2
plasma membrane part (GO:0044459)	1.95	2	CALCR, LRP5
extracellular exosome (GO:0070062)	1.89	2	WNT1, COL1A2

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
collagen type I trimer (GO:0005584)	-	9.11	0.0	COL1A2, COL1A1
receptor complex (GO:0043235)	-	4.01	0.012	VDR, CALCR, COL1A2, LRP5
extracellular space (GO:0005615)	-	2.63	0.03	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
fibrillar collagen trimer (GO:0005583)	-	7.32	0.0	COL1A2, COL1A1
endoplasmic reticulum lumen (GO:0005788)	-	4.5	0.001	WNT1, COL1A1, COL1A2
organelle lumen (GO:0043233)	-	3.05	0.025	LRP5, CALCR, WNT1, COL1A1, COL1A2
dendrite (GO:0030425)	NEW	3.92	0.024	VDR, CALCR, COL1A1, LRP5
extracellular matrix (GO:0031012)	-	3.81	0.004	WNT1, COL1A1, LRP5, COL1A2
intracellular organelle lumen (GO:0070013)	-	3.05	0.024	WNT1, COL1A1, COL1A2
extracellular region (GO:0005576)	-	2.18	0.042	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
membrane-enclosed lumen (GO:0031974)	-	3.05	0.036	LRP5, CALCR, WNT1, COL1A1, COL1A2
endoplasmic reticulum part (GO:0044432)	-	2.73	0.007	VDR, LRP5, WNT1, COL1A1, CALCR, COL1A2
extracellular matrix part (GO:0044420)	-	4.97	0.032	COL1A2, COL1A1
proteinaceous extracellular matrix (GO:0005578)	-	4.01	0.007	WNT1, COL1A1, LRP5, COL1A2
collagen trimer (GO:0005581)	-	5.21	0.017	COL1A2, COL1A1