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Atlas / Disease / Colorectal adenoma

Colorectal adenoma

disease
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Also known as adenoma of large boweladenoma of large intestineadenoma of the large boweladenoma of the large intestinecolorectum adenomalarge bowel adenoma

Summary

Colorectal adenoma (MONDO:0005484) is a cancer with 75 cohort genes (151 GWAS associations across 4 studies; 13 CIViC-evidence somatic drivers; 13 ClinVar predisposition records) and 140 clinical trials. The dominant Reactome pathway is Formation of definitive endoderm (4 cohort genes). Top therapeutic interventions include calcitriol, icosapent ethyl, and linaclotide.

At a glance

  • Classification: Cancer
  • Cohort genes: 75
  • GWAS associations: 151
  • ClinVar variants: 13
  • Clinical trials: 140

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecolorectal adenoma
Mondo IDMONDO:0005484
EFOEFO:0005406
DOIDDOID:0050860, DOID:0050914
NCITC5673
SNOMED CT399432003
UMLSC1302401
MedGen224904
Anatomy (UBERON)UBERON:0012652
Is cancer (heuristic)yes

Also known as: adenoma of large bowel · adenoma of large intestine · adenoma of the large bowel · adenoma of the large intestine · colorectal adenoma · colorectum adenoma · large bowel adenoma

Data availability: 13 ClinVar variants · 151 GWAS associations (4 studies) · 5 GenCC gene-disease records · 16 cell lines.

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › digestive system disorder › intestinal disorder › intestinal neoplasm › colorectal neoplasm › colorectal adenoma

Related subtypes (8): rectal neoplasm, colorectal leiomyoma, colonic neoplasm, colorectal cancer, colorectal gastrointestinal stromal tumor, colorectal hamartoma, colorectal neuroendocrine tumor G1, small intestinal intraepithelial neoplasia

Subtypes (4): colon adenoma, rectum adenoma, colorectal sessile serrated adenoma/polyp, colorectal tubulovillous adenoma

Genetics & variants

GWAS landscape

151 GWAS associations across 4 studies. Top hits map to 36 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs118743924e-74SMAD7A1.17
rs69832673e-64PCAT1, CASC8, POU5F1B, CCAT2G1.16
rs70132782e-56POU5F1B, PCAT1, CASC8T1.15
rs22935819e-40GREM1-AS1, GREM1A1.15
rs586587716e-37SCG5 - GREM1A1.15
rs168927664e-32LINC00536 - EIF3HC1.2
rs30879672e-31POU2AF2T1.12
rs17416401e-26LAMA5C1.12
rs27359405e-25TERT - MIR4457G1.09
rs123727182e-23ATF1G1.09
rs288407504e-23RHPN2T1.21
rs1895831e-22FGFR3P3 - CASC20G1.1
rs351071392e-22BMP4C1.09
rs112558412e-21RNA5SP299 - LINC02676T1.09
rs125145174e-21RNU1-150P - TTC33A1.1
rs71219581e-20POLD3G1.08
rs32178104e-19CCND2T1.13
rs613890911e-18CHRDL2C1.23
rs759549263e-18METRNL - RPL23AP87G1.09
rs9943085e-18CASC20 - LINC01713C1.08
rs7040175e-18ZMIZ1-AS1G1.08
rs32178741e-17CCND2T1.08
rs354702711e-16RPS27P4 - MRPS31P1G1.1
rs1170791422e-16UTP23A1.19
rs66785172e-16LAMC1A1.08
rs5978083e-16ATXN2G1.08
rs170111416e-16LINC01705G1.09
rs127084914e-15SCG5 - GREM1G1.07
rs49762705e-15PITX1-AS1C1.07
rs60668256e-15PREX1A1.07

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST007856Huyghe JR201855,10565,079Discovery of common and rare genetic risk variants for colorectal cancer.
GCST005151Hofer P20176364,294Bayesian and frequentist analysis of an Austrian genome-wide association study of colorectal cancer and advanced adenomas.
GCST005153Hofer P20176360Bayesian and frequentist analysis of an Austrian genome-wide association study of colorectal cancer and advanced adenomas.
GCST002212Wang J20131391,267Germline variants and advanced colorectal adenomas: adenoma prevention with celecoxib trial genome-wide association study.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR3
Tier 3: regulatory4
Tier 4: intronic/intergenic42

MAF distribution

BucketVariants
common (>=0.05)47
low_freq (0.01-0.05)2
rare (<0.01)1
unknown0

Functional consequences

ConsequenceCount
intron_variant28
intergenic_variant10
non_coding_transcript_exon_variant4
regulatory_region_variant4
3_prime_UTR_variant2
5_prime_UTR_variant1
missense_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs118743921848926786A>G,T0.455intron_variantSMAD74e-74Tier 4: intronic/intergenic
rs69832678127401060G>T0.477non_coding_transcript_exon_variantPCAT1, CASC8, POU5F1B, CCAT23e-64Tier 4: intronic/intergenic
rs70132788127402647T>C,G0.376intron_variantPOU5F1B, PCAT1, CASC82e-56Tier 4: intronic/intergenic
rs22935811532718535G>A,C,T0.212non_coding_transcript_exon_variantGREM1-AS1, GREM19e-40Tier 4: intronic/intergenic
rs586587711532709533T>A,C,G0.194intergenic_variantSCG5 - GREM16e-37Tier 4: intronic/intergenic
rs168927668116618444A>C0.083regulatory_region_variantLINC00536 - EIF3H4e-32Tier 3: regulatory
rs308796711111286111T>A,C,G0.2913_prime_UTR_variantPOU2AF22e-31Tier 2: splice/UTR
rs17416402062357358T>A,C,G0.235intron_variantLAMA51e-26Tier 4: intronic/intergenic
rs273594051296371A>G,T0.495non_coding_transcript_exon_variantTERT - MIR44575e-25Tier 4: intronic/intergenic
rs123727181250777307A>G,T0.392intron_variantATF12e-23Tier 4: intronic/intergenic
rs288407501933029021T>G0.052intron_variantRHPN24e-23Tier 4: intronic/intergenic
rs189583206395810G>A,C,T0.33intergenic_variantFGFR3P3 - CASC201e-22Tier 4: intronic/intergenic
rs351071391453952388A>C,G,T0.4235_prime_UTR_variantBMP42e-22Tier 2: splice/UTR
rs11255841108697617T>A0.297intergenic_variantRNA5SP299 - LINC026762e-21Tier 4: intronic/intergenic
rs12514517540279974G>A0.288intergenic_variantRNU1-150P - TTC334e-21Tier 4: intronic/intergenic
rs71219581174568967T>A,G0.49intergenic_variantPOLD31e-20Tier 4: intronic/intergenic
rs3217810124279105C>A,T0.125intron_variantCCND24e-19Tier 4: intronic/intergenic
rs613890911174716876C>G,T0.039intron_variantCHRDL21e-18Tier 4: intronic/intergenic
rs759549261783104098A>C,G,T0.353regulatory_region_variantMETRNL - RPL23AP873e-18Tier 3: regulatory
rs994308206622975C>A,G,T0.406intergenic_variantCASC20 - LINC017135e-18Tier 4: intronic/intergenic
rs7040171079059375A>G0.415intron_variantZMIZ1-AS15e-18Tier 4: intronic/intergenic
rs3217874124291642C>G,T0.428intron_variantCCND21e-17Tier 4: intronic/intergenic
rs35470271340873748A>G0.154intron_variantRPS27P4 - MRPS31P11e-16Tier 4: intronic/intergenic
rs1170791428116778675C>A0.043intron_variantUTP232e-16Tier 4: intronic/intergenic
rs66785171183033504A>C,G,T0.41intron_variantLAMC12e-16Tier 4: intronic/intergenic
rs59780812111535554A>C,G,T0.483intron_variantATXN23e-16Tier 4: intronic/intergenic
rs170111411221939292A>G0.209intron_variantLINC017056e-16Tier 4: intronic/intergenic
rs127084911532700635G>A0.413intergenic_variantSCG5 - GREM14e-15Tier 4: intronic/intergenic
rs49762705135131530C>T0.45intron_variantPITX1-AS15e-15Tier 4: intronic/intergenic
rs60668252048723580A>G,T0.355intron_variantPREX16e-15Tier 4: intronic/intergenic

ClinVar germline variants

13 retrieved; paginated sample, class counts are floors:

10 conflicting classifications of pathogenicity, 1 benign/likely benign, 1 benign, 1 uncertain significance

ClinVarVariant (HGVS)GeneClassificationReview
127295NM_000038.6(APC):c.4360A>G (p.Lys1454Glu)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
133510NM_000038.6(APC):c.4237A>G (p.Met1413Val)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
135716NM_000038.6(APC):c.6985A>G (p.Ile2329Val)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
135724NM_000038.6(APC):c.8266A>G (p.Ile2756Val)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
141047NM_000038.6(APC):c.8383G>A (p.Ala2795Thr)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
141928NM_000038.6(APC):c.449A>G (p.Lys150Arg)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
161205NM_000038.6(APC):c.7778A>G (p.Asn2593Ser)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
161206NM_000038.6(APC):c.2847G>T (p.Met949Ile)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
41503NM_000038.6(APC):c.3479C>A (p.Thr1160Lys)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
41536NM_000038.6(APC):c.7717A>G (p.Ile2573Val)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
140839NM_000038.6(APC):c.4732T>G (p.Cys1578Gly)APCUncertain significancereviewed by expert panel
127294NM_000038.6(APC):c.4336G>A (p.Ala1446Thr)APCBenign/Likely benigncriteria provided, multiple submitters, no conflicts
133530NM_000038.6(APC):c.4420G>A (p.Ala1474Thr)APCBenignreviewed by expert panel

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 41 · Orphanet: 92 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 1

Dual-evidence genes (GWAS + Mendelian — highest-confidence targets)

GeneHGNCEvidence routes
APCAPCGWAS, Orphanet

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
APCLoFAML,ANSC,CHOL,COAD,COADREAD,CSCC,EGC,ESCA,ESCC,HCC,LUAD,MEL,MT,NETNOS,NSCLC,PRAD,PROSTATE,READ,STAD,STOMACH,UM,VULVACIViC #66
BRIP1CIViC #15955
AXIN1LoFESCA,GBM,HCC
TBX3ActBRCA,COADREAD,DLBCLNOS
TCF7L2LoFCOAD,COADREAD,HCC,READ
TERTActPRCCCIViC #79
CCND2LoFAML,CLLSLLCIViC #9
YAP1CIViC #8292
CDH1LoFBLCA,BRCA,CSCC,DLBCLNOS,ESCA,STADCIViC #888
RHPN2LoFBRCA,LUAD,LUSC
FAT3ActANGS,BRCA,CCRCC,CHOL,CLLSLL,COAD,COADREAD,DLBCLNOS,HNSC,LUSC,MEL,NETNOS,PAAD,PANCREAS,PRAD,RCC,READ,SIC,STAD,STOMACH,WDTC
CTNNB1ActACC,COAD,COADREAD,ESCA,HCC,LIHB,LUAD,MBL,MEL,NSCLC,OVT,PAST,PRAD,PROSTATE,RMS,SKIN,SOFT_TISSUE,STAD,UCEC,WTCIViC #1290
SH2B3ActMDSCIViC #7954

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
AXIN1LimitedAutosomal dominantcolorectal adenoma3
BRF1LimitedAutosomal dominantcolorectal adenoma6
BRIP1LimitedAutosomal dominantcolorectal adenoma10
DSC2LimitedAutosomal dominantcolorectal adenoma7
DSC3LimitedAutosomal dominantcolorectal adenoma12
ZSWIM7LimitedUnknowncolorectal adenoma3

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
APCOrphanet:220460Attenuated familial adenomatous polyposis
APCOrphanet:2615845q22 microdeletion syndrome
APCOrphanet:314022Gastric adenocarcinoma and proximal polyposis of the stomach
APCOrphanet:3258Cenani-Lenz syndrome
APCOrphanet:873Desmoid tumor
BRF1Orphanet:444072Cerebellar-facial-dental syndrome
BRIP1Orphanet:145Hereditary breast and/or ovarian cancer syndrome
BRIP1Orphanet:84Fanconi anemia
ZSWIM7Orphanet:24346,XX gonadal dysgenesis
ZSWIM7Orphanet:399805Male infertility with azoospermia or oligozoospermia due to single gene mutation
DSC2Orphanet:293888Inherited isolated arrhythmogenic cardiomyopathy, dominant-left variant
DSC2Orphanet:293899Inherited isolated arrhythmogenic ventricular dysplasia, biventricular variant
DSC2Orphanet:293910Inherited isolated arrhythmogenic cardiomyopathy, dominant-right variant
DSC3Orphanet:217407Hereditary hypotrichosis with recurrent skin vesicles
AXIN1Orphanet:210159Adult hepatocellular carcinoma
BMP2Orphanet:26129520p12.3 microdeletion syndrome
BMP2Orphanet:93396Brachydactyly type A2
BMP4Orphanet:139471Microphthalmia with brain and digit anomalies
BMP4Orphanet:199306Cleft lip/palate
BMP4Orphanet:828Stickler syndrome
BMP4Orphanet:93100Renal agenesis, unilateral
BMPR1BOrphanet:2098Acromesomelic dysplasia, Grebe type
BMPR1BOrphanet:2639Fibular aplasia-complex brachydactyly syndrome
BMPR1BOrphanet:93384Brachydactyly type C
BMPR1BOrphanet:93388Brachydactyly type A1
BMPR1BOrphanet:93396Brachydactyly type A2
TBX3Orphanet:3138Ulnar-mammary syndrome
TCF7L2Orphanet:528084Non-specific syndromic intellectual disability
TERCOrphanet:1775Dyskeratosis congenita
TERCOrphanet:2032Idiopathic pulmonary fibrosis
TERCOrphanet:88Idiopathic aplastic anemia
TERTOrphanet:146Differentiated thyroid carcinoma
TERTOrphanet:1501Adrenocortical carcinoma
TERTOrphanet:1775Dyskeratosis congenita
TERTOrphanet:2032Idiopathic pulmonary fibrosis
TERTOrphanet:2495Meningioma
TERTOrphanet:3322Hoyeraal-Hreidarsson syndrome
TERTOrphanet:457246Clear cell sarcoma of kidney
TERTOrphanet:618Familial melanoma
TERTOrphanet:88Idiopathic aplastic anemia
TGFB1Orphanet:1328Camurati-Engelmann disease
TGFB1Orphanet:565788Infantile inflammatory bowel disease with neurological involvement
TGFB1Orphanet:586Cystic fibrosis
MYRFOrphanet:647811Cardiac-urogenital syndrome
ITCHOrphanet:228426Syndromic multisystem autoimmune disease due to Itch deficiency
CCND2Orphanet:83473Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
YAP1Orphanet:1473Uveal coloboma-cleft lip and palate-intellectual disability
YAP1Orphanet:157791Epithelioid hemangioendothelioma
ZMIZ1Orphanet:528084Non-specific syndromic intellectual disability
CDH1Orphanet:1331Familial prostate cancer

Cohort genes → proteins

75 cohort genes, 72 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only68
gwas_and_clinvar1
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
APCHGNC:583ENSG00000134982P25054Adenomatous polyposis coli proteingwas,clinvar
BRF1HGNC:11551ENSG00000185024Q92994Transcription factor IIIB 90 kDa subunitgencc
BRIP1HGNC:20473ENSG00000136492Q9BX63Fanconi anemia group J proteingencc
ZSWIM7HGNC:26993ENSG00000214941Q19AV6Zinc finger SWIM domain-containing protein 7gencc
DSC2HGNC:3036ENSG00000134755Q02487Desmocollin-2gencc
DSC3HGNC:3037ENSG00000134762Q14574Desmocollin-3gencc
AXIN1HGNC:903ENSG00000103126O15169Axin-1gencc
RNF4HGNC:10067ENSG00000063978P78317E3 ubiquitin-protein ligase RNF4gwas
CNNM1HGNC:102ENSG00000119946Q9NRU3Metal transporter CNNM1gwas
RPS21HGNC:10409ENSG00000171858P63220Small ribosomal subunit protein eS21gwas
BMP2HGNC:1069ENSG00000125845P12643Bone morphogenetic protein 2gwas
BMP4HGNC:1071ENSG00000125378P12644Bone morphogenetic protein 4gwas
BMP5HGNC:1072ENSG00000112175P22003Bone morphogenetic protein 5gwas
BMPR1BHGNC:1077ENSG00000138696O00238Bone morphogenetic protein receptor type-1Bgwas
TBX3HGNC:11602ENSG00000135111O15119T-box transcription factor TBX3gwas
TCF7L2HGNC:11641ENSG00000148737Q9NQB0Transcription factor 7-like 2gwas
TEAD3HGNC:11716ENSG00000007866Q99594Transcriptional enhancer factor TEF-5gwas
TERCHGNC:11727ENSG00000270141telomerase RNA componentgwas
TERTHGNC:11730ENSG00000164362O14746Telomerase reverse transcriptasegwas
TGFB1HGNC:11766ENSG00000105329P01137Transforming growth factor beta-1 proproteingwas
MYRFHGNC:1181ENSG00000124920Q9Y2G1Myelin regulatory factorgwas
WNT8BHGNC:12789ENSG00000075290Q93098Protein Wnt-8bgwas
MYO1GHGNC:13880ENSG00000136286B0I1T2Unconventional myosin-Iggwas
ITCHHGNC:13890ENSG00000078747Q96J02E3 ubiquitin-protein ligase Itchy homologgwas
MYNNHGNC:14955ENSG00000085274Q9NPC7Myoneuringwas
DYNLRB1HGNC:15468ENSG00000125971Q9NP97Dynein light chain roadblock-type 1gwas
PIGUHGNC:15791ENSG00000101464Q9H490GPI-anchor transamidase component PIGUgwas
CCND2HGNC:1583ENSG00000118971P30279G1/S-specific cyclin-D2gwas
TP53INP2HGNC:16104ENSG00000078804Q8IXH6Tumor protein p53-inducible nuclear protein 2gwas
YAP1HGNC:16262ENSG00000137693P46937Transcriptional coactivator YAP1gwas
ZMIZ1HGNC:16493ENSG00000108175Q9ULJ6Zinc finger MIZ domain-containing protein 1gwas
CD9HGNC:1709ENSG00000010278P21926CD9 antigengwas
BOCHGNC:17173ENSG00000144857Q9BWV1Brother of CDOgwas
LRIG1HGNC:17360ENSG00000144749Q96JA1Leucine-rich repeats and immunoglobulin-like domains protein 1gwas
TBRG4HGNC:17443ENSG00000136270Q969Z0FAST kinase domain-containing protein 4gwas
CDH1HGNC:1748ENSG00000039068P12830Cadherin-1gwas
DACT1HGNC:17748ENSG00000165617Q9NYF0Dapper homolog 1gwas
VTI1AHGNC:17792ENSG00000151532Q96AJ9Vesicle transport through interaction with t-SNAREs homolog 1Agwas
NXNHGNC:18008ENSG00000167693Q6DKJ4Nucleoredoxingwas
RAB40BHGNC:18284ENSG00000141542Q12829Ras-related protein Rab-40Bgwas
SMARCAD1HGNC:18398ENSG00000163104Q9H4L7SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1gwas
STARD13HGNC:19164ENSG00000133121Q9Y3M8StAR-related lipid transfer protein 13gwas
RHPN2HGNC:19974ENSG00000131941Q8IUC4Rhophilin-2gwas
GREM1HGNC:2001ENSG00000166923O60565Gremlin-1gwas
POLD3HGNC:20932ENSG00000077514Q15054DNA polymerase delta subunit 3gwas
SATB2HGNC:21637ENSG00000119042Q9UPW6DNA-binding protein SATB2gwas
CCM2HGNC:21708ENSG00000136280Q9BSQ5Cerebral cavernous malformations 2 proteingwas
COX15HGNC:2263ENSG00000014919Q7KZN9Heme A synthase COX15gwas
MED13LHGNC:22962ENSG00000123066Q71F56Mediator of RNA polymerase II transcription subunit 13-likegwas
NANOS1HGNC:23044ENSG00000188613Q8WY41Nanos homolog 1gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
APCAdenomatous polyposis coli proteinTumor suppressor.
BRF1Transcription factor IIIB 90 kDa subunitGeneral activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters.
BRIP1Fanconi anemia group J proteinDNA-dependent ATPase and 5’-3’ DNA helicase required for the maintenance of chromosomal stability.
ZSWIM7Zinc finger SWIM domain-containing protein 7Involved in early stages of the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents.
DSC2Desmocollin-2A component of desmosome cell-cell junctions which are required for positive regulation of cellular adhesion.
DSC3Desmocollin-3A component of desmosome cell-cell junctions which are required for positive regulation of cellular adhesion.
AXIN1Axin-1Component of the beta-catenin destruction complex required for regulating CTNNB1 levels through phosphorylation and ubiquitination, and modulating Wnt-signaling.
RNF4E3 ubiquitin-protein ligase RNF4E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates ‘Lys-6’-, ‘Lys-11’-, ‘Lys-48’- and ‘Lys-63’-linked polyubiquitination of those substrates and their subsequent targeting to the prot…
CNNM1Metal transporter CNNM1Probable metal transporter.
RPS21Small ribosomal subunit protein eS21Component of the small ribosomal subunit.
BMP2Bone morphogenetic protein 2Growth factor of the TGF-beta superfamily that plays essential roles in many developmental processes, including cardiogenesis, neurogenesis, and osteogenesis.
BMP4Bone morphogenetic protein 4Growth factor of the TGF-beta superfamily that plays essential roles in many developmental processes, including neurogenesis, vascular development, angiogenesis and osteogenesis.
BMP5Bone morphogenetic protein 5Growth factor of the TGF-beta superfamily that plays essential roles in many developmental processes, including cartilage and bone formation or neurogenesis.
BMPR1BBone morphogenetic protein receptor type-1BOn ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases.
TBX3T-box transcription factor TBX3Transcriptional repressor involved in developmental processes.
TCF7L2Transcription factor 7-like 2Participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner.
TEAD3Transcriptional enhancer factor TEF-5Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis.
TERTTelomerase reverse transcriptaseTelomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes.
TGFB1Transforming growth factor beta-1 proproteinTransforming growth factor beta-1 proprotein: Precursor of the Latency-associated peptide (LAP) and Transforming growth factor beta-1 (TGF-beta-1) chains, which constitute the regulatory and active subunit of TGF-beta-1, respectively.
MYRFMyelin regulatory factorConstitutes a precursor of the transcription factor.
WNT8BProtein Wnt-8bLigand for members of the frizzled family of seven transmembrane receptors.
MYO1GUnconventional myosin-IgUnconventional myosin required during immune response for detection of rare antigen-presenting cells by regulating T-cell migration.
ITCHE3 ubiquitin-protein ligase Itchy homologActs as an Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.
DYNLRB1Dynein light chain roadblock-type 1Component of dynein, a family of motor proteins essential for movement along microtubules.
PIGUGPI-anchor transamidase component PIGUComponent of the glycosylphosphatidylinositol-anchor (GPI-anchor) transamidase (GPI-T) complex that catalyzes the formation of the linkage between a proprotein and a GPI-anchor and participates in GPI anchored protein biosynthesis.
CCND2G1/S-specific cyclin-D2Regulatory component of the cyclin D2-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition.
TP53INP2Tumor protein p53-inducible nuclear protein 2Dual regulator of transcription and autophagy.
YAP1Transcriptional coactivator YAP1Transcriptional regulator with dual roles as a coactivator and corepressor.
ZMIZ1Zinc finger MIZ domain-containing protein 1Acts as a transcriptional coactivator.
CD9CD9 antigenIntegral membrane protein associated with integrins, which regulates different processes, such as sperm-egg fusion, platelet activation and aggregation, and cell adhesion.
BOCBrother of CDOComponent of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells.
LRIG1Leucine-rich repeats and immunoglobulin-like domains protein 1Acts as a feedback negative regulator of signaling by receptor tyrosine kinases, through a mechanism that involves enhancement of receptor ubiquitination and accelerated intracellular degradation.
TBRG4FAST kinase domain-containing protein 4Plays a role in processing of mitochondrial RNA precursors and in stabilization of a subset of mature mitochondrial RNA species, such as MT-CO1, MT-CO2, MT-CYB, MT-CO3, MT-ND3, MT-ND5 and MT-ATP8/6.
CDH1Cadherin-1Cadherins are calcium-dependent cell adhesion proteins.
DACT1Dapper homolog 1Involved in regulation of intracellular signaling pathways during development.
VTI1AVesicle transport through interaction with t-SNAREs homolog 1AV-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane.
NXNNucleoredoxinFunctions as a redox-dependent negative regulator of the Wnt signaling pathway, possibly by preventing ubiquitination of DVL3 by the BCR(KLHL12) complex.
RAB40BRas-related protein Rab-40BRAB40B small GTPase acts as substrate-recognition components of the ECS(RAB40B) E3 ubiquitin ligase complex which mediates the ubiquitination of target proteins.
SMARCAD1SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1Protein that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization.
STARD13StAR-related lipid transfer protein 13GTPase-activating protein for RhoA, and perhaps for Cdc42.
RHPN2Rhophilin-2Binds specifically to GTP-Rho.
GREM1Gremlin-1Cytokine that may play an important role during carcinogenesis and metanephric kidney organogenesis, as a BMP antagonist required for early limb outgrowth and patterning in maintaining the FGF4-SHH feedback loop.
POLD3DNA polymerase delta subunit 3Accessory component of both the DNA polymerase delta complex and the DNA polymerase zeta complex.
SATB2DNA-binding protein SATB2Binds to DNA, at nuclear matrix- or scaffold-associated regions.
CCM2Cerebral cavernous malformations 2 proteinComponent of the CCM signaling pathway which is a crucial regulator of heart and vessel formation and integrity.
COX15Heme A synthase COX15Catalyzes the second reaction in the biosynthesis of heme A, a prosthetic group of mitochondrial cytochrome c oxidase (CcO).
MED13LMediator of RNA polymerase II transcription subunit 13-likeComponent of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes.
NANOS1Nanos homolog 1May act as a translational repressor which regulates translation of specific mRNAs by forming a complex with PUM2 that associates with the 3’-UTR of mRNA targets.
FAT3Protocadherin Fat 3May play a role in the interactions between neurites derived from specific subsets of neurons during development.
TMBIM1Protein lifeguard 3Negatively regulates aortic matrix metalloproteinase-9 (MMP9) production and may play a protective role in vascular remodeling.

Protein-family classification

Druggable: 10 · Difficult: 16 · Unknown: 49 · Druggable fraction: 0.13

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Other/Unknown491.2×0.480
Scaffold/PPI61.4×0.867
Phosphatase11.1×0.867
Transcription factor101.1×0.867
Protease21.0×0.867
Antibody/Immunoglobulin20.8×0.867
Kinase20.7×0.867
Enzyme (other)30.5×0.955

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
APCOther/UnknownnoArmadillo, APC_rpt, SAMP
BRF1Transcription factornoTFIIB, BRF1_TBP-bd_dom, Znf_TFIIB
BRIP1Enzyme (other)yes3.6.4.12Helicase-like_DEXD_c2, ATP-dep_Helicase_C, RAD3-like_helicase_DEAD
ZSWIM7Transcription factornoZnf_SWIM
DSC2Other/UnknownnoCadherin_Y-type_LIR, Cadherin-like_dom, Desmosomal_cadherin
DSC3Other/UnknownnoCadherin_Y-type_LIR, Cadherin-like_dom, Desmosomal_cadherin
AXIN1Other/UnknownnoDIX, Axin_b-cat-bd, RGS
RNF4Transcription factornoZnf_RING, Znf_RING/FYVE/PHD, Znf_RING_CS
CNNM1Other/UnknownnoCBS_dom, CNNM, Ion_transp-like_CBS
RPS21Other/UnknownnoRibosomal_eS21, Ribosomal_eS21_CS, Ribosomal_eS21_sf
BMP2Other/UnknownnoTGF-b_propeptide, TGF-b_C, TGF-beta-like
BMP4Other/UnknownnoTGF-b_propeptide, TGF-b_C, TGF-beta-like
BMP5Other/UnknownnoTGF-b_propeptide, TGF-b_C, TGF-beta-like
BMPR1BKinaseyes2.7.10.2TGFB_receptor, Activin_recp, Prot_kinase_dom
TBX3Transcription factornoTF_T-box, p53-like_TF_DNA-bd_sf, TF_T-box_CS
TCF7L2Other/UnknownnoHMG_box_dom, CTNNB1-bd_N, TCF/LEF
TEAD3Other/UnknownnoTEA/ATTS_dom, TEF_metazoa, TEF-5
TERCOther/Unknownno
TERTOther/UnknownnoRT_dom, Telomerase_RT, Telomerase_RBD
TGFB1Other/UnknownnoTGF-b_propeptide, TGF-b_C, TGFb1
MYRFTranscription factornop53-like_TF_DNA-bd_sf, NDT80_DNA-bd_dom, MYRF_C2
WNT8BOther/UnknownnoWnt, Wnt8, Wnt_CS
MYO1GOther/UnknownnoMyosin_head_motor_dom-like, Myosin_TH1, P-loop_NTPase
ITCHScaffold/PPIno2.3.2.26C2_dom, HECT_dom, WW_dom
MYNNTranscription factornoBTB/POZ_dom, SKP1/BTB/POZ_sf, Znf_C2H2_type
DYNLRB1Other/UnknownnoRoadblock/LAMTOR2_dom, DYNLRB1/2
PIGUOther/UnknownnoPIG-U
CCND2Other/UnknownnoCyclin_C-dom, Cyclin_N, Cyclin-like_dom
TP53INP2Other/UnknownnoTP53INP
YAP1Scaffold/PPInoWW_dom, WW_dom_sf, YAP1
ZMIZ1Transcription factornoZnf_MIZ, Znf_RING/FYVE/PHD, ZMIZ1_N
CD9Other/UnknownnoTetraspanin_animals, Tetraspanin_EC2_sf, Tetraspanin/Peripherin
BOCAntibody/ImmunoglobulinyesIg_sub2, Ig_sub, FN3_dom
LRIG1Antibody/ImmunoglobulinyesLRRNT, Cys-rich_flank_reg_C, Leu-rich_rpt
TBRG4KinaseyesFAST_Leu-rich, FAST_2, RAP
CDH1Other/UnknownnoCadherin_Y-type_LIR, Cadherin-like_dom, Cadherin_pro_dom
DACT1Other/UnknownnoDapper
VTI1AOther/UnknownnoT_SNARE_dom, Vesicle_trsprt_v-SNARE_N, SNARE
NXNOther/UnknownnoThioredoxin-like_fold, Thioredoxin_domain, Thioredoxin-like_sf
RAB40BOther/UnknownnoSOCS_box, Small_GTPase, Small_GTP-bd
SMARCAD1Other/UnknownnoSNF2_N, Helicase_C-like, CUE
STARD13Other/UnknownnoRhoGAP_dom, SAM, START_lipid-bd_dom
RHPN2Scaffold/PPInoPDZ, BRO1_dom, HR1_rho-bd
GREM1Other/UnknownnoDAN_dom, Cys_knot_C, Gremlin-1/2
POLD3Other/UnknownnoPOLD3, POLD3_sf
SATB2Transcription factornoHD, CUT_dom, Homeodomain-like_sf
CCM2Other/UnknownnoPTB/PI_dom, PH-like_dom_sf, Malcavernin
COX15ProteaseyesCOX15/CtaA_fam, Peptidase_S1_PA, HemeA_synthase_2
MED13LOther/UnknownnoMed13_C, Mediator_Med13_N, MID_MedPIWI
NANOS1Transcription factornoNanos/Xcar2, Znf_nanos-typ, Nanos_sf

Expression context

Cohort genes with no expression data: 0.

66 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)75
unknown0

Top tissues across cohort

TissueCohort genes
male germ line stem cell (sensu Vertebrata) in testis7
pancreatic ductal cell7
ventricular zone6
calcaneal tendon6
granulocyte5
mucosa of transverse colon5
inferior vagus X ganglion5
secondary oocyte5
right uterine tube4
cauda epididymis4
buccal mucosa cell4
adrenal tissue4
sural nerve3
primordial germ cell in gonad3
tendon of biceps brachii3
gingival epithelium3
lower esophagus mucosa3
middle temporal gyrus3
oocyte3
bronchial epithelial cell3

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
APC297ubiquitousmarkersubstantia nigra pars compacta, substantia nigra pars reticulata, medial globus pallidus
BRF1198ubiquitousmarkersural nerve, right uterine tube, right hemisphere of cerebellum
BRIP1181ubiquitousmarkerventricular zone, primordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis
ZSWIM7250ubiquitousmarkertendon of biceps brachii, right adrenal gland cortex, left adrenal gland
DSC2256ubiquitousmarkergingival epithelium, gingiva, oral cavity
DSC3177broadmarkerupper leg skin, gingival epithelium, gingiva
AXIN1175ubiquitousmarkergranulocyte, mucosa of transverse colon, lower esophagus mucosa
RNF4297ubiquitousmarkerthymus, oocyte, middle temporal gyrus
CNNM1176broadmarkerpostcentral gyrus, prefrontal cortex, parietal lobe
RPS21295ubiquitousmarkernipple, penis, trabecular bone tissue
BMP2238broadmarkercartilage tissue, pancreatic ductal cell, pigmented layer of retina
BMP4189ubiquitousmarkerpigmented layer of retina, retina, rectum
BMP5153broadmarkercalcaneal tendon, islet of Langerhans, cartilage tissue
BMPR1B239broadmarkercalcaneal tendon, bronchial epithelial cell, cauda epididymis
TBX3243ubiquitousmarkerright adrenal gland cortex, right adrenal gland, adrenal cortex
TCF7L2291ubiquitousmarkerlateral nuclear group of thalamus, endothelial cell, pancreatic ductal cell
TEAD3247ubiquitousmarkermuscle layer of sigmoid colon, lower esophagus, lower esophagus muscularis layer
TERC113ubiquitousyesbone marrow cell, colonic epithelium, male germ line stem cell (sensu Vertebrata) in testis
TERT105broadyesstromal cell of endometrium, type B pancreatic cell, olfactory bulb
TGFB1204ubiquitousmarkergranulocyte, monocyte, leukocyte
MYRF223ubiquitousmarkermiddle frontal gyrus, C1 segment of cervical spinal cord, inferior vagus X ganglion
WNT8B33tissue_specificyesdiaphragm, tendon of biceps brachii, buccal mucosa cell
MYO1G203broadmarkergranulocyte, monocyte, leukocyte
ITCH275ubiquitousmarkersperm, male germ cell, calcaneal tendon
MYNN274ubiquitousmarkerbuccal mucosa cell, secondary oocyte, male germ line stem cell (sensu Vertebrata) in testis
DYNLRB1159ubiquitousmarkerBrodmann (1909) area 9, right frontal lobe, anterior cingulate cortex
PIGU240ubiquitousmarkermucosa of transverse colon, ganglionic eminence, ventricular zone
CCND2293ubiquitousmarkeradrenal tissue, seminal vesicle, cauda epididymis
TP53INP2256ubiquitousmarkerinferior vagus X ganglion, lateral globus pallidus, globus pallidus
YAP1279ubiquitousmarkersaphenous vein, germinal epithelium of ovary, cauda epididymis

Protein interactions among cohort

Intra-cohort edges: 34.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CTNNB115,668
CDH18,738
TGFB17,596
YAP16,742
RNF45,804
TERT5,717
POLR3A4,915
FKBP54,900
FEN14,897
BMP44,425

Intra-cohort edges

ABSources
APCAXIN1biogrid_interaction, intact, string_interaction
APCCTNNB1intact, string_interaction
AXIN1CTNNB1biogrid_interaction, intact, string_interaction
AXIN1TCF7L2string_interaction
AXIN1YAP1intact
BMP2BMPR1Bbiogrid_interaction, intact
BMP2GREM1string_interaction
BMP4BMP5intact
BMP4GREM1string_interaction
BOCCTNNB1biogrid_interaction
CDH1CTNNB1biogrid_interaction, intact, string_interaction
CDH1LRIG1string_interaction
CDH1MYNNintact
CLPTM1LTERTstring_interaction
CTNNB1DACT1intact, string_interaction
CTNNB1DSC3biogrid_interaction
CTNNB1FAT3string_interaction
CTNNB1FOXL1string_interaction
CTNNB1TBX3biogrid_interaction
CTNNB1TCF7L2biogrid_interaction, intact, string_interaction
CTNNB1TERTstring_interaction
CTNNB1WNT8Bstring_interaction
CTNNB1YAP1string_interaction
CTNNB1ZMIZ1biogrid_interaction
DIP2BPOU2AF2string_interaction
DIP2BPOU2AF3string_interaction
EIF3HPOU2AF3string_interaction
EIF3HRHPN2string_interaction
FEN1MYRFstring_interaction
FOXL1SMARCAD1intact
MYNNRHPN2string_interaction
POLD3POU2AF3string_interaction
POU2AF2POU2AF3string_interaction
TEAD3YAP1biogrid_interaction, intact, string_interaction

Structural data

PDB: 45 · AlphaFold-only: 27 · No structure: 3

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
RPS21P63220209
FKBP5Q13451138
CTNNB1P3522250
YAP1P4693741
APCP2505431
POLR3AO1480229
FEN1P3974828
EIF3HO1537227
DYNLRB1Q9NP9724
TERTO1474623
DUSP10Q9Y6W623
AXIN1O1516922
CDH1P1283022
BMP2P1264321
TGFB1P0113720
PREX1Q8TCU614
ITCHQ96J0212
TEAD3Q9959410
POLD3Q150549
CCM2Q9BSQ58
TP53INP2Q8IXH67
CD9P219265
PIGUQ9H4904
SMARCAD1Q9H4L74
BRIP1Q9BX633
DSC2Q024873
RNF4P783173
TCF7L2Q9NQB03
BOCQ9BWV13
STARD13Q9Y3M83

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
FADS1O6042794.82
HEXDQ8WVB393.50
ZSWIM7Q19AV692.13
NXNQ6DKJ490.37
B9D2Q9BPU989.79
MYO1GB0I1T288.42
CDPF1Q6NVV787.30
COX15Q7KZN985.29
VTI1AQ96AJ985.00
WNT8BQ9309884.88
BMP4P1264479.12
DIP2BQ9P26578.83
CLPTM1LQ96KA578.54
TMBIM1Q969X177.32
RAB40BQ1282976.36
DSC3Q1457475.53
BMP5P2200374.85
BRF1Q9299470.22
PLEKHG6Q3KR1668.36
CNNM1Q9NRU367.07
FOXL1Q1295264.30
SH2B3Q9UQQ263.45
GPATCH1Q9BRR859.51
MED13LQ71F5656.79
DACT1Q9NYF050.95
COLCA1Q6ZS6237.18
FAT3Q8TDW7

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 477. Enrichment computed across 96 evidence-associated genes (66 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 66 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Formation of definitive endoderm443.3×3e-04TCF7L2, CDH1, CTNNB1, SMAD3
TCF dependent signaling in response to WNT712.5×3e-04APC, TCF7L2, TERT, WNT8B, CTNNB1, MYC, AXIN1
Signal Transduction213.2×3e-04APC, BMP2, BMPR1B, TCF7L2, TERT, TGFB1, ITCH, BOC (+13 more)
Transcriptional regulation by RUNX3520.6×5e-04TCF7L2, TEAD3, TGFB1, SMAD3, MYC
Binding of TCF/LEF:CTNNB1 to target gene promoters351.9×0.001TCF7L2, CTNNB1, MYC
RUNX3 regulates WNT signaling351.9×0.001TCF7L2, CTNNB1, MYC
Deubiquitination611.3×0.001APC, TGFB1, SMAD3, SMAD7, MYC, AXIN1
Signaling by TGFB family members610.5×0.001BMP2, BMPR1B, TGFB1, SMAD3, SMAD7, MYC
Signaling by WNT610.2×0.001APC, TCF7L2, TERT, MYC, AXIN1, PRKG1
Disassembly of the destruction complex and recruitment of AXIN to the membrane421.6×0.002APC, WNT8B, CTNNB1, AXIN1
Formation of axial mesoderm337.1×0.002YAP1, CTNNB1, SMAD3
Signaling by GSK3beta mutants334.6×0.002APC, CTNNB1, AXIN1
CTNNB1 S33 mutants aren’t phosphorylated334.6×0.002APC, CTNNB1, AXIN1
CTNNB1 S37 mutants aren’t phosphorylated334.6×0.002APC, CTNNB1, AXIN1
CTNNB1 S45 mutants aren’t phosphorylated334.6×0.002APC, CTNNB1, AXIN1
CTNNB1 T41 mutants aren’t phosphorylated334.6×0.002APC, CTNNB1, AXIN1
Gene expression (Transcription)133.5×0.002BMP2, BRF1, TCF7L2, TEAD3, TGFB1, ITCH, CCND2, SATB2 (+5 more)
Beta-catenin phosphorylation cascade330.5×0.003APC, CTNNB1, AXIN1
Germ layer formation at gastrulation330.5×0.003BMP4, CTNNB1, SMAD3
Gastrulation415.7×0.003BMP4, TCF7L2, CDH1, SMAD3
Formation of the nephric duct328.8×0.003BMP4, CTNNB1, GATA3
RNA Polymerase II Transcription113.8×0.003BMP2, TCF7L2, TEAD3, TGFB1, ITCH, CCND2, SATB2, SMAD3 (+3 more)
Signaling by WNT in cancer327.3×0.003APC, TCF7L2, AXIN1
PCNA-Dependent Long Patch Base Excision Repair323.6×0.005POLD3, FEN1, RFC3
Signaling by Receptor Tyrosine Kinases75.5×0.005ITCH, LRIG1, SH2B3, LAMA5, LAMC1, MYC, ATF1
Loss of Function of TGFBR1 in Cancer269.2×0.006TGFB1, SMAD3
Signaling by TGF-beta Receptor Complex412.1×0.006TGFB1, SMAD3, SMAD7, MYC
Regulation of PD-L1(CD274) transcription58.2×0.006TCF7L2, TEAD3, YAP1, CTNNB1, MYC
Loss of Function of SMAD2/3 in Cancer257.7×0.007TGFB1, SMAD3
Signaling by TGF-beta Receptor Complex in Cancer257.7×0.007TGFB1, SMAD3

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 87 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of transcription by RNA polymerase II233.9×1e-05RNF4, BMP2, BMP4, BMP5, BMPR1B, TBX3, TCF7L2, TEAD3 (+15 more)
positive regulation of epithelial cell proliferation719.6×4e-05BMP4, BMP5, TCF7L2, TGFB1, YAP1, LAMC1, MYC
positive regulation of epithelial to mesenchymal transition621.9×1e-04BMP2, BMP4, TCF7L2, TGFB1, CTNNB1, SMAD3
odontogenesis of dentin-containing tooth620.8×1e-04BMP2, BMP4, TGFB1, CTNNB1, LAMA5, NKX2-3
in utero embryonic development108.3×1e-04BMP2, TBX3, ZMIZ1, NXN, CCM2, CTNNB1, DSC3, GATA3 (+2 more)
positive regulation of miRNA transcription620.0×1e-04BMP2, TERT, TGFB1, GATA3, SMAD3, MYC
canonical Wnt signaling pathway712.3×3e-04TCF7L2, TGFB1, WNT8B, YAP1, CTNNB1, GATA3, AXIN1
positive regulation of SMAD protein signal transduction522.0×5e-04BMP2, BMP4, BMP5, TGFB1, SMAD3
branching involved in ureteric bud morphogenesis521.1×5e-04BMP2, BMP4, CTNNB1, LAMA5, MYC
positive regulation of odontoblast differentiation383.0×6e-04BMP2, BMP4, CTNNB1
SMAD protein signal transduction433.7×6e-04ZMIZ1, SMAD3, SMAD7, MAP1LC3A
negative regulation of cell population proliferation115.3×7e-04APC, BMP2, BMP4, BMP5, TGFB1, CD9, CTNNB1, SH2B3 (+3 more)
negative regulation of fat cell differentiation517.9×8e-04BMP2, TGFB1, YAP1, SMAD3, AXIN1
negative regulation of canonical Wnt signaling pathway79.5×8e-04APC, BMP2, TCF7L2, DACT1, GREM1, CTNNB1, AXIN1
pericardium development364.6×8e-04BMP2, CCM2, SMAD3
endoderm development428.7×8e-04BMP4, TGFB1, LAMC1, SMAD3
embryonic hindlimb morphogenesis426.7×0.001BMP4, TBX3, CTNNB1, PITX1
negative regulation of vascular associated smooth muscle cell migration358.1×0.001BMP4, PRKG1, PTPN1
cellular response to BMP stimulus425.8×0.001BMP2, BMP4, BMPR1B, GATA3
regulation of epithelial to mesenchymal transition352.8×0.001GREM1, CTNNB1, SMAD7
cell fate specification424.2×0.001APC, TBX3, CTNNB1, NKX2-3
positive regulation of branching involved in lung morphogenesis2193.7×0.001BMP4, CTNNB1
regulation of nephron tubule epithelial cell differentiation2193.7×0.001CTNNB1, GATA3
positive regulation of primary miRNA processing2193.7×0.001BMP4, TGFB1
endocardial cushion formation348.4×0.001BMP2, BMP5, TBX3
negative regulation of platelet aggregation348.4×0.001CD9, SH2B3, PRKG1
ureteric bud development420.9×0.002BMP4, TGFB1, SMAD3, SMAD7
positive regulation of osteoblast differentiation512.9×0.002BMP2, BMP4, BMPR1B, YAP1, CTNNB1
positive regulation of cell population proliferation114.2×0.002BMP2, BMP4, BMP5, TBX3, TGFB1, CCND2, TBRG4, GREM1 (+3 more)
positive regulation of DNA-templated transcription123.9×0.002RNF4, BMP2, BMP4, TGFB1, MYRF, TP53INP2, YAP1, CDH1 (+4 more)

Therapeutics

Drugs indicated for this disease

0 approved, 4 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
CalciumPhase 3 (in late-stage trials)
CelecoxibPhase 3 (in late-stage trials)
CholecalciferolPhase 3 (in late-stage trials)
RofecoxibPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Aspirin, Berberine, Doconexent, Icosapent, Icosapent Ethyl, Linaclotide, Mesalamine.

Drug target analysis

Approved (phase 4): 6 · Phase ≥3: 6 · Phased (≥1): 9 · Undrugged: 66

Druggability breadth: 43 of 96 evidence-associated genes (45%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
RPS21GENTAMICIN SULFATE
BMPR1BMOMELOTINIB
TERTBERBERINE
CCND2PALBOCICLIB
CTNNB1DITHIAZANINE IODIDE
FKBP5TACROLIMUS ANHYDROUS

Top cohort targets by molecule count

SymbolMoleculesMax phase
BMPR1B284
TERT104
CTNNB144
CCND234
FKBP534
RPS2114
TEAD312
TGFB112
MYO1G12
APC00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
GENTAMICIN SULFATE4RPS21
MOMELOTINIB4BMPR1B
FEDRATINIB4BMPR1B
AXITINIB4BMPR1B
RUXOLITINIB4BMPR1B
VANDETANIB4BMPR1B
GILTERITINIB4BMPR1B
PAZOPANIB4BMPR1B
SUNITINIB4BMPR1B
DASATINIB4BMPR1B
QUIZARTINIB4BMPR1B
CRIZOTINIB4BMPR1B
BERBERINE4TERT
DOXORUBICIN4TERT
PALBOCICLIB4CCND2
DITHIAZANINE IODIDE4CTNNB1
TACROLIMUS ANHYDROUS4FKBP5
SIROLIMUS4FKBP5
SARACATINIB3BMPR1B
LINIFANIB3BMPR1B
CANERTINIB3BMPR1B
ALVOCIDIB3BMPR1B, CCND2
LESTAURTINIB3BMPR1B
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
QUERCETIN3CTNNB1
SU-0148132BMPR1B
R-4062BMPR1B
AT-92832BMPR1B

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 6.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
TERT391Binding:389, Functional:2
CTNNB1361Binding:358, Functional:3
BMPR1B166Binding:164, ADMET:2
YAP1135Binding:135
RPS2190Binding:90
TEAD339Binding:39
FKBP538Binding:38
CCND228Binding:28
APC24Binding:24
BMP222Binding:18, Functional:4
TCF7L222Binding:22
FADS121Binding:21
CDH118Binding:18
FEN115Binding:12, Functional:3
AXIN111Binding:11
DUSP1010Binding:9, ADMET:1
TGFB19Binding:9
MYO1G7Binding:7
SATB26Binding:6
RNF43Binding:3
BMP42Binding:2
ITCH2Binding:2
MYNN2Binding:2
HEXD2Binding:2
BRF11Binding:1
TBRG41Binding:1
POLD31Binding:1
COX151Binding:1
CLPTM1L1Binding:1
EIF3H1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
BRIP13.6.4.12DNA helicase
BMPR1B2.7.10.2non-specific protein-tyrosine kinase
ITCH2.3.2.26, 2.3.2.B8HECT-type E3 ubiquitin transferase,
DUSP103.1.3.16, 3.1.3.48protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
FADS11.14.19.30acyl-lipid (8-3)-desaturase
FEN13.1.99.B1

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
BMPR1B166
TERT391
YAP1135
CTNNB1361

Pharmacogenomics

Cohort genes with a PharmGKB record: 72; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Drug repurposing candidates

30 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

CompoundMax phaseCohort target (bioactivity)
GENTAMICIN SULFATE4RPS21
MOMELOTINIB4BMPR1B
FEDRATINIB4BMPR1B
AXITINIB4BMPR1B
RUXOLITINIB4BMPR1B
VANDETANIB4BMPR1B
GILTERITINIB4BMPR1B
PAZOPANIB4BMPR1B
SUNITINIB4BMPR1B
DASATINIB4BMPR1B
QUIZARTINIB4BMPR1B
CRIZOTINIB4BMPR1B
BERBERINE4TERT
DOXORUBICIN4TERT
PALBOCICLIB4CCND2
DITHIAZANINE IODIDE4CTNNB1
TACROLIMUS ANHYDROUS4FKBP5
SIROLIMUS4FKBP5
SARACATINIB3BMPR1B
LINIFANIB3BMPR1B
CANERTINIB3BMPR1B
ALVOCIDIB3BMPR1B, CCND2
LESTAURTINIB3BMPR1B
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
QUERCETIN3CTNNB1
SU-0148132BMPR1B
R-4062BMPR1B
AT-92832BMPR1B

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)6RPS21, BMPR1B, TERT, CCND2, CTNNB1, FKBP5
BPhased (≥1) drug, not yet approved3TEAD3, TGFB1, MYO1G
CDruggable family + PDB, no drug7BRIP1, BOC, LRIG1, TBRG4, DUSP10, EIF3H, FEN1
DDruggable family + AlphaFold only, no drug2COX15, FADS1
EDifficult family or no structure, no drug57APC, BRF1, ZSWIM7, DSC2, DSC3, AXIN1, RNF4, CNNM1, BMP2, BMP4 (+47 more)

Undrugged target profiles

66 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
YAP1135CTNNB1
APC24CTNNB1
AXIN111CTNNB1
TCF7L222CTNNB1
CDH118CTNNB1
CLPTM1L1TERT
BRF11—
BRIP10—
ZSWIM70—
DSC20—
DSC30—
RNF43—
CNNM10—
BMP222—
BMP42—
BMP50—
TBX30—
TERC0—
MYRF0—
WNT8B0—
ITCH2—
MYNN2—
DYNLRB10—
PIGU0—
TP53INP20—
ZMIZ10—
CD90—
BOC0—
LRIG10—
TBRG41—

Clinical trials & evidence

Clinical trials

Clinical trials: 140.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified118
PHASE28
PHASE34
PHASE2/PHASE34
PHASE13
PHASE42
PHASE1/PHASE21

Top trials by phase / activity

NCTPhaseStatusTitle
NCT07167342PHASE4RECRUITINGThe Effect of Oral Clostridium Butyricum on the Recurrence After Colonoscopic Resection of Colorectal Adenoma
NCT01767870PHASE4UNKNOWNEfficacy Combined Fecal Immunochemical Test-Sigmoidoscopy for the Detection of Advanced Colorectal Neoplasia
NCT07505056PHASE3NOT_YET_RECRUITINGJianpi Lishi Jiedu Granules for Prevention of Postoperative Recurrence in Colorectal Advanced Adenomas
NCT00141193PHASE3COMPLETEDPrevention of Colorectal Sporadic Adenomatous Polyps (PRESAP)
NCT00282386PHASE3COMPLETEDA Study to Evaluate the Effect of MK0966 (Rofecoxib) on the Recurrence of Colorectal Adenomas (0966-122)
NCT01437826PHASE3TERMINATEDAntioxidant Supplement and Reduction of Metachronous Adenomas of the Large Bowel: a Double Blind Randomized Trial
NCT02143505PHASE2/PHASE3UNKNOWNStudy of Calcium Plus Vitamin D Supplementation in Prevention of Colorectal Adenomas Recurrence
NCT02226185PHASE2/PHASE3COMPLETEDStudy of Berberine Hydrochloride in Prevention of Colorectal Adenomas Recurrence
NCT03281096PHASE2/PHASE3COMPLETEDA Research of Berberine Hydrochloride to Prevent Colorectal Adenomas in Patients With Previous Colorectal Cancer
NCT03333265PHASE2/PHASE3COMPLETEDPrimary Chemoprevention of Familial Adenomatous Polyposis With Berberine Hydrochloride
NCT02134925PHASE2ACTIVE_NOT_RECRUITINGVaccine Therapy in Treating Patients With Newly Diagnosed Advanced Colon Polyps
NCT02965703PHASE2ACTIVE_NOT_RECRUITINGAspirin in Preventing Colorectal Cancer in Patients With Colorectal Adenoma
NCT03796884PHASE2ACTIVE_NOT_RECRUITINGLinaclotide in Treating Patients With Stages 0-3 Colorectal Cancer
NCT06205862PHASE2RECRUITINGEfficacy and Safety of Fecal Microbiota Transplantation (FMT) in Reducing Recurrence of Colorectal Adenoma (CRA)
NCT06612281PHASE2RECRUITINGEvaluation of Gixam’s Performance in a FIT Negative Population
NCT06722950PHASE2NOT_YET_RECRUITINGPhase II Clinical Study of AC591 in Preventing Oxaliplatin-Induced Peripheral Neuropathy
NCT00582660PHASE2COMPLETEDEvaluation of Surgically Resected Colorectal Adenomas and Carcinomas After 7 Days Pretreatment With Celecoxib
NCT04216251PHASE1/PHASE2COMPLETEDPRevention Using EPA Against coloREctal Cancer
NCT05402124PHASE2UNKNOWNThe Colorectal Cancer Chemoprevention Acceleration and Improvement Platform (CRC-CHAMP) Study
NCT07095517PHASE1RECRUITINGPathways, Risk Factors, and mOleculeS to Prevent Early-onset Colorectal Tumors
NCT00298545PHASE1COMPLETEDEffect of Vitamin D and Calcium on Genes in the Colon
NCT04952129PHASE1COMPLETEDOptimal Selenium for Bowel Polyps (OSCAR)
NCT01538550Not specifiedACTIVE_NOT_RECRUITINGPilot Study of a National Screening Programme for Bowel Cancer in Norway
NCT04185779Not specifiedRECRUITINGCOLO-COHORT (Colorectal Cancer Cohort) Study
NCT05144152Not specifiedRECRUITINGDiagnostic Accuracy of M3 in Predicting Colorectal Advanced Adenoma Recurrence (M3-AA)
NCT05381792Not specifiedRECRUITINGSerial Gut Microbiome and Bacterial Gene Markers Changes After Endoscopic Resection of Colorectal Advanced Neoplasia
NCT05405673Not specifiedRECRUITINGDiagnostic Accuracy of a Panel of Bacterial Gene Markers (M3) for Colorectal Advanced Neoplasia
NCT05592886Not specifiedRECRUITINGA Novel Oral Synbiotic Formula in Reducing Advanced Adenoma Recurrence and Colorectal Neoplasia-related Bacterial Gene Markers
NCT05612347Not specifiedRECRUITINGColonoscopy vs Stool Testing for Older Adults With Colon Polyps
NCT05636085Not specifiedNOT_YET_RECRUITINGClinical Performance of the Mainz Biomed Colorectal Cancer Screening Test for Colorectal Cancer and Advanced Adenoma
NCT05638542Not specifiedACTIVE_NOT_RECRUITINGComparison of Expression of Carcinogenesis-related Molecular Markers in the Patients With Colon Cancer and Polyp
NCT05653960Not specifiedNOT_YET_RECRUITINGClinical Outcomes After EMR or ESD of Colorectal Neoplasms - A Multicenter Registry
NCT05877456Not specifiedENROLLING_BY_INVITATIONValidation of the Global Polypectomy Assessment Tool (GPAT)
NCT05988645Not specifiedRECRUITINGPerformance and Safety of MiWEndo-assisted Colonoscopy (MiWEndo II)
NCT06067620Not specifiedNOT_YET_RECRUITINGRobotic Right Hemicolectomy Versus Laparoscopic Right Hemicolectomy
NCT06133387Not specifiedRECRUITINGPARADIGM - En Bloc Trial With the EndoQuest Endoluminal Surgical (ELS) System
NCT06136026Not specifiedNOT_YET_RECRUITINGIntegrated Chinese and Western Medicine Specialized Disease Cohort for Colorectal Cancer
NCT06307938Not specifiedRECRUITINGCirculating Tumor DNA in Patients Summoned for Colonoscopy; - a Liquid Biopsy for Detection, Characterization, Individualized Treatment and Follow-up of Colorectal Cancer
NCT06452745Not specifiedRECRUITINGEarly Diagnosis of Colorectal Cancer Based on a Non-invasive Metabolomics Profile
NCT06629051Not specifiedRECRUITING6-year Follow-up Data After the Berberine Intervention Trial

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
CALCITRIOL41
ICOSAPENT ETHYL41
LINACLOTIDE41
SELENOMETHIONINE41
BLOOD, WHOLE31
GINGER31
BERBERINE CHLORIDE15
METHYLSELENOCYSTEINE11
CHEMBL44323201
CHEMBL147451701

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclinical_trialsclinvarctd_gene_interactiondbsnpdepmapdiamond_similaritydoidefoensemblentrezesm2_similarityfantom5_genefantom5_promotergenccgenerifgogtopdbgtopdb_interactiongwasgwas_studyhgncintactinterprointogenmedgenmeshmimmondomondochildmondoparentncitorphanetpatentpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assayreactomerefseqrhearnacentralsctidscxa_expressionscxa_gene_experimentsignorstring_interactiontranscriptuberonufeatureumlsuniprot