Cancer CRCdb

TF information

TF name:	HOXA3
TF family:	Homeobox
Ensembl gene ID:	ENSG00000105997
Ensembl protein ID:	ENSP00000379640, ENSP00000324884, ENSP00000484411
Entrez gene ID:	3200

Database name	Link	Database name	Link
NCBI Gene:		Genecards:
Uniprot:		Wikipedia:
Cosmic 3D:		Geneontology:
CCLE:

Frequency of HOXA3 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_069	Cell line	Brain	SF268	0.50381679389313
Sample_02_114	Cell line	Mammary Gland	CAL51	0.75879396984925
Sample_02_179	Cell line	Urinary bladder	T24	0.16091954022989
Sample_02_227	Cell line	Oesophagus	TE7	0.08
Sample_02_268	Cell line	Kidney	A-498	0.50544581871885
Sample_02_361	Cell line	Colon	HT29_DMSO	0.12035398230088

HOXA3 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name
Sample_02_114	Mammary Gland	Cell line	CAL51
Sample_02_268	Kidney	Cell line	A-498

HOXA3 distribution in all CRCs

Genomic distribution of SEs associated with HOXA3

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Mutation of HOXA3

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Database name	Link
gnomAD:	gnomAD
ExAC:	ExAC
ICGC:

Database name	Link
Cosmic:
Cosmic cell lines:
Depmap:

TCGA somatic mutations and clinical variants of HOXA3

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
rs140908739	chr7	27147774	27147774	G	A	exonic	HOXA3	synonymous	LUSC\|1\|178\|0.00562
-	chr7	27148062	27148062	G	A	exonic	HOXA3	synonymous	BRCA\|2\|982\|0.00204
-	chr7	27150188	27150188	G	T	exonic	HOXA3	nonsynonymous	TGCT\|1\|155\|0.00645
-	chr7	27148158	27148158	C	A	exonic	HOXA3	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27150214	27150214	A	G	exonic	HOXA3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27150165	27150165	G	T	exonic	HOXA3	nonsynonymous	LUSC\|1\|178\|0.00562
rs746145258	chr7	27150085	27150085	C	T	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27148287	27148287	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27148282	27148282	C	-	exonic	HOXA3	frameshift	LUAD\|3\|543\|0.00552
-	chr7	27148311	27148311	C	T	exonic	HOXA3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27147796	27147796	G	T	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27155873	27155873	G	A	intronic	HOXA3	unknown	BRCA\|1\|982\|0.00102
rs750383849	chr7	27148052	27148052	-	G	exonic	HOXA3	frameshift	BRCA\|1\|982\|0.00102,KIPAN\|2\|799\|0.00250,KIRC\|2\|451\|0.00443,PAAD\|1\|185\|0.00541
-	chr7	27147975	27147975	G	A	exonic	HOXA3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27150230	27150230	C	G	exonic	HOXA3	synonymous	CESC\|1\|194\|0.00515
-	chr7	27147915	27147915	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27147556	27147556	G	T	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27148122	27148122	C	T	exonic	HOXA3	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27150131	27150131	G	A	exonic	HOXA3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27148097	27148097	T	C	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27148264	27148264	G	C	exonic	HOXA3	nonsynonymous	LUSC\|1\|178\|0.00562
rs753346052	chr7	27149826	27149826	-	G	exonic	HOXA3	frameshift	LUAD\|1\|543\|0.00184
-	chr7	27147572	27147572	C	T	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
rs371241609	chr7	27147599	27147599	C	T	exonic	HOXA3	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27147987	27147987	C	T	exonic	HOXA3	synonymous	PAAD\|1\|185\|0.00541,STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147487	27147487	A	T	UTR3	HOXA3	unknown	BRCA\|1\|982\|0.00102
-	chr7	27148069	27148069	C	T	exonic	HOXA3	nonsynonymous	BRCA\|1\|982\|0.00102,PAAD\|1\|185\|0.00541
-	chr7	27149927	27149927	G	A	exonic	HOXA3	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27148082	27148082	G	C	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27147954	27147954	G	T	exonic	HOXA3	synonymous	LUAD\|3\|543\|0.00552
-	chr7	27149906	27149906	C	A	exonic	HOXA3	synonymous	HNSC\|1\|512\|0.00195
-	chr7	27149788	27149788	A	G	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27147982	27147982	G	-	exonic	HOXA3	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27148284	27148284	C	T	exonic	HOXA3	synonymous	UCEC\|1\|248\|0.00403
-	chr7	27148002	27148005	CGGG	-	exonic	HOXA3	frameshift	BLCA\|1\|396\|0.00253
rs370472758	chr7	27147736	27147736	T	C	exonic	HOXA3	nonsynonymous	SKCM\|2\|368\|0.00543
-	chr7	27147911	27147911	A	T	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27149901	27149901	G	-	exonic	HOXA3	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147667	27147667	C	-	exonic	HOXA3	frameshift	ACC\|1\|90\|0.01111
-	chr7	27147873	27147873	C	T	exonic	HOXA3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27148121	27148121	C	T	exonic	HOXA3	nonsynonymous	SKCM\|2\|368\|0.00543
-	chr7	27149901	27149901	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27148265	27148265	C	T	exonic	HOXA3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27147796	27147796	G	C	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27149908	27149908	C	T	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27149789	27149789	G	T	exonic	HOXA3	synonymous	LUAD\|2\|543\|0.00368
-	chr7	27147792	27147792	T	C	exonic	HOXA3	synonymous	PAAD\|1\|185\|0.00541
-	chr7	27148083	27148083	-	C	exonic	HOXA3	frameshift	KIPAN\|2\|799\|0.00250,KIRC\|2\|451\|0.00443
-	chr7	27147795	27147795	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27148090	27148090	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27147453	27147454	AA	-	UTR3	HOXA3	unknown	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27148074	27148074	T	C	exonic	HOXA3	synonymous	SKCM\|2\|368\|0.00543
-	chr7	27148273	27148273	T	C	exonic	HOXA3	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr7	27150148	27150148	C	T	exonic	HOXA3	nonsynonymous	PAAD\|1\|185\|0.00541
rs747916069	chr7	27147966	27147966	G	A	exonic	HOXA3	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27147939	27147939	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27147900	27147900	C	T	exonic	HOXA3	synonymous	UCEC\|1\|248\|0.00403
-	chr7	27147998	27147998	C	T	exonic	HOXA3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr7	27150097	27150097	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
rs770556616	chr7	27147616	27147616	G	A	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27148046	27148046	C	T	exonic	HOXA3	nonsynonymous	PAAD\|1\|185\|0.00541
-	chr7	27147767	27147767	C	T	exonic	HOXA3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147572	27147572	C	A	exonic	HOXA3	stopgain	LUAD\|1\|543\|0.00184
-	chr7	27149780	27149780	T	A	exonic	HOXA3	nonsynonymous	SARC\|1\|247\|0.00405
-	chr7	27148004	27148004	G	A	exonic	HOXA3	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr7	27147963	27147963	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27149875	27149875	G	C	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27147548	27147548	G	A	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27148061	27148061	C	T	exonic	HOXA3	nonsynonymous	PRAD\|1\|499\|0.00200
rs369217098	chr7	27149900	27149900	C	A	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27147827	27147827	G	T	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27149775	27149775	G	A	exonic	HOXA3	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr7	27148164	27148164	C	A	exonic	HOXA3	nonsynonymous	ACC\|1\|90\|0.01111
-	chr7	27148262	27148262	G	A	exonic	HOXA3	stopgain	PRAD\|1\|499\|0.00200
rs773785595	chr7	27147688	27147688	G	A	exonic	HOXA3	nonsynonymous	CESC\|1\|194\|0.00515
-	chr7	27148137	27148137	G	T	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27149779	27149779	C	T	exonic	HOXA3	nonsynonymous	SARC\|1\|247\|0.00405
-	chr7	27150193	27150193	C	T	exonic	HOXA3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27148128	27148128	G	T	exonic	HOXA3	stopgain	LUAD\|1\|543\|0.00184
-	chr7	27147924	27147924	C	T	exonic	HOXA3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253,UCEC\|1\|248\|0.00403
-	chr7	27148329	27148329	G	T	exonic	HOXA3	stopgain	LUAD\|1\|543\|0.00184
-	chr7	27148028	27148028	T	A	exonic	HOXA3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr7	27148113	27148113	C	T	exonic	HOXA3	synonymous	ESCA\|1\|185\|0.00541
rs756450304	chr7	27149829	27149829	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27150227	27150227	C	T	exonic	HOXA3	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27147656	27147656	G	A	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27148056	27148056	G	A	exonic	HOXA3	synonymous	LUSC\|1\|178\|0.00562
rs764656757	chr7	27150136	27150136	C	T	exonic	HOXA3	nonsynonymous	CESC\|1\|194\|0.00515,COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27148210	27148210	G	A	exonic	HOXA3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27147830	27147830	C	T	exonic	HOXA3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27149809	27149809	C	T	exonic	HOXA3	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr7	27150111	27150111	C	A	exonic	HOXA3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr7	27148070	27148070	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27149875	27149875	G	T	exonic	HOXA3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr7	27150147	27150147	G	C	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27150132	27150132	C	T	exonic	HOXA3	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27150139	27150139	C	T	exonic	HOXA3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27149773	27149773	G	A	exonic	HOXA3	stopgain	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27148111	27148111	C	T	exonic	HOXA3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27148297	27148297	G	A	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27147988	27147988	G	T	exonic	HOXA3	stopgain	LUAD\|1\|543\|0.00184
-	chr7	27147884	27147884	G	A	exonic	HOXA3	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355,PRAD\|1\|499\|0.00200
-	chr7	27150221	27150221	G	A	exonic	HOXA3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147727	27147727	G	T	exonic	HOXA3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27149900	27149900	C	T	exonic	HOXA3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147855	27147855	C	A	exonic	HOXA3	synonymous	LUAD\|1\|543\|0.00184
rs761726531	chr7	27147961	27147961	-	G	exonic	HOXA3	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27147685	27147685	C	T	exonic	HOXA3	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr7	27147768	27147768	G	A	exonic	HOXA3	synonymous	LUAD\|2\|543\|0.00368
rs760414819	chr7	27150120	27150120	C	T	exonic	HOXA3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27148122	27148122	C	A	exonic	HOXA3	nonsynonymous	UCEC\|1\|248\|0.00403

Disease information of HOXA3

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
HOXA3	Malignant neoplasm of breast	C04;C17	Neoplastic Process	UNIPROT
HOXA3	Congenital Heart Defects	C14;C16	Congenital Abnormality	CTD_human
HOXA3	Liver Cirrhosis, Experimental	C06	Experimental Model of Disease	CTD_human
HOXA3	Craniofacial Abnormalities	C05;C16	Congenital Abnormality	CTD_human
HOXA3	Lymphatic Abnormalities	C15;C16	Anatomical Abnormality	CTD_human

Pathway associated with HOXA3

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number

Go term information of HOXA3

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GO_term_name	GO_term_type	TF_name
GO_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT	BP	HOXA3
GO_THYMUS_DEVELOPMENT	BP	HOXA3
GO_CRANIAL_NERVE_MORPHOGENESIS	BP	HOXA3
GO_CRANIAL_NERVE_DEVELOPMENT	BP	HOXA3
GO_ORGAN_FORMATION	BP	HOXA3
GO_NERVE_DEVELOPMENT	BP	HOXA3
GO_BLOOD_VESSEL_REMODELING	BP	HOXA3
GO_REGIONALIZATION	BP	HOXA3
GO_THYROID_GLAND_DEVELOPMENT	BP	HOXA3
GO_HMG_BOX_DOMAIN_BINDING	MF	HOXA3

Survival analysis of HOXA3

Methods

Overall Survival

Disease Free Survival (RFS)

Group Cutoff

Median

Quartile

Custom

Cutoff-High(%)

Hazards Ratio (HR) Calculate the hazards ratio based on Cox PH Model.

95% Confidence Interval Add the 95% CI as dotted line.

Axis Units

Expression of HOXA3

Pan cancer (TCGA) Cell line (ENCODE) In vitro differentiated cell (ENCODE) Primary cell (ENCODE) Tissue (NCBI) Normal tissue (GTEx) Cell line (CCLE)