Cancer CRCdb

TF information

TF name:	HOXA2
TF family:	Homeobox
Ensembl gene ID:	ENSG00000105996
Ensembl protein ID:	ENSP00000222718
Entrez gene ID:	3199

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

Frequency of HOXA2 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_069	Cell line	Brain	SF268	0.25190839694656
Sample_02_114	Cell line	Mammary Gland	CAL51	0.8643216080402
Sample_02_208	Cell line	Stomach	YCC3	0.125

HOXA2 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_208	Stomach	Cell line	YCC3

HOXA2 distribution in all CRCs

Genomic distribution of SEs associated with HOXA2

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Mutation of HOXA2

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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 HOXA2

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
rs772212707	chr7	27140368	27140368	C	T	exonic	HOXA2	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs140022054	chr7	27140675	27140675	G	A	exonic	HOXA2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27140593	27140593	G	A	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27141044	27141044	C	A	exonic	HOXA2	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs777207853	chr7	27142044	27142044	G	A	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27141877	27141877	G	A	exonic	HOXA2	synonymous	UCEC\|1\|248\|0.00403
-	chr7	27140961	27140961	C	T	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27140705	27140705	A	-	exonic	HOXA2	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27141063	27141063	C	A	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140995	27140995	C	A	exonic	HOXA2	stopgain	UCEC\|1\|248\|0.00403
rs749965554	chr7	27141045	27141045	C	T	exonic	HOXA2	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr7	27140534	27140534	A	C	exonic	HOXA2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27142065	27142065	C	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140478	27140478	C	T	exonic	HOXA2	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr7	27141938	27141938	G	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27141033	27141033	G	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
rs748975641	chr7	27141056	27141056	G	A	exonic	HOXA2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27140938	27140938	G	T	exonic	HOXA2	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27140891	27140891	C	T	exonic	HOXA2	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27142031	27142031	T	A	exonic	HOXA2	nonsynonymous	GBM\|1\|290\|0.00345,GBMLGG\|1\|820\|0.00122
-	chr7	27142096	27142096	C	T	exonic	HOXA2	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27140753	27140753	C	T	exonic	HOXA2	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27140754	27140754	C	A	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140514	27140514	G	C	exonic	HOXA2	nonsynonymous	CESC\|1\|194\|0.00515
-	chr7	27140486	27140486	T	C	exonic	HOXA2	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27140828	27140828	G	A	exonic	HOXA2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27140643	27140643	G	A	exonic	HOXA2	nonsynonymous	BLCA\|1\|396\|0.00253
rs762714236	chr7	27141760	27141760	T	G	exonic	HOXA2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27141906	27141906	G	A	exonic	HOXA2	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr7	27142001	27142001	G	A	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27140431	27140431	C	T	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27140542	27140542	C	T	exonic	HOXA2	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr7	27140602	27140602	G	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140420	27140420	T	A	exonic	HOXA2	synonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr7	27140524	27140524	C	T	exonic	HOXA2	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr7	27140752	27140752	C	T	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27141032	27141032	A	T	exonic	HOXA2	synonymous	LUSC\|1\|178\|0.00562
-	chr7	27140762	27140762	G	A	exonic	HOXA2	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs143043350	chr7	27140497	27140497	C	T	exonic	HOXA2	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27140535	27140535	G	T	exonic	HOXA2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27142045	27142045	A	-	exonic	HOXA2	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27141071	27141071	G	A	exonic	HOXA2	synonymous	OV\|1\|469\|0.00213
-	chr7	27141788	27141788	G	A	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140492	27140492	G	A	exonic	HOXA2	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27140404	27140404	T	C	exonic	HOXA2	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|2\|489\|0.00409,OV\|1\|469\|0.00213,READ\|1\|122\|0.00820
rs138940688	chr7	27140509	27140509	G	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27142065	27142065	C	A	exonic	HOXA2	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr7	27140390	27140390	A	-	exonic	HOXA2	frameshift	STAD\|2\|395\|0.00506,STES\|2\|395\|0.00506
-	chr7	27140817	27140817	G	A	exonic	HOXA2	nonsynonymous	BRCA\|1\|982\|0.00102
rs758080122	chr7	27140466	27140466	G	A	exonic	HOXA2	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr7	27141754	27141754	G	T	exonic	HOXA2	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27141898	27141898	C	T	exonic	HOXA2	synonymous	LUAD\|1\|543\|0.00184
-	chr7	27140419	27140419	C	A	exonic	HOXA2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27140803	27140803	C	T	exonic	HOXA2	nonsynonymous	BLCA\|1\|396\|0.00253
rs372854321	chr7	27140770	27140770	C	T	exonic	HOXA2	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27141985	27141985	C	T	exonic	HOXA2	synonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr7	27140789	27140789	C	G	exonic	HOXA2	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr7	27140382	27140382	G	A	exonic	HOXA2	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr7	27140891	27140891	C	A	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140493	27140493	A	-	exonic	HOXA2	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27141898	27141898	-	T	exonic	HOXA2	frameshift	LUAD\|1\|543\|0.00184
rs762322767	chr7	27140422	27140422	C	T	exonic	HOXA2	nonsynonymous	BRCA\|1\|982\|0.00102
rs750882072	chr7	27141768	27141768	T	C	exonic	HOXA2	nonsynonymous	STAD\|2\|395\|0.00506,STES\|2\|395\|0.00506
-	chr7	27140362	27140362	G	A	exonic	HOXA2	stopgain	SKCM\|1\|368\|0.00272
-	chr7	27140804	27140804	C	A	exonic	HOXA2	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27141772	27141772	G	A	exonic	HOXA2	synonymous	CESC\|1\|194\|0.00515
rs774102766	chr7	27142034	27142034	G	T	exonic	HOXA2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27142023	27142023	G	A	exonic	HOXA2	stopgain	BLCA\|1\|396\|0.00253
-	chr7	27141923	27141923	C	T	exonic	HOXA2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27140626	27140626	G	T	exonic	HOXA2	nonsynonymous	LUAD\|6\|543\|0.01105
-	chr7	27140855	27140855	G	A	exonic	HOXA2	synonymous	SKCM\|1\|368\|0.00272
-	chr7	27140448	27140448	C	T	exonic	HOXA2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr7	27140784	27140784	G	A	exonic	HOXA2	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27142050	27142050	A	T	exonic	HOXA2	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr7	27141067	27141067	C	T	exonic	HOXA2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr7	27140427	27140427	C	T	exonic	HOXA2	nonsynonymous	PAAD\|1\|185\|0.00541
-	chr7	27141905	27141905	C	T	exonic	HOXA2	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr7	27142053	27142053	T	A	exonic	HOXA2	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr7	27141085	27141085	C	A	splicing	HOXA2	splicing	UCEC\|1\|248\|0.00403
-	chr7	27140389	27140389	-	A	exonic	HOXA2	frameshift	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr7	27140577	27140577	G	T	exonic	HOXA2	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr7	27140435	27140435	G	T	exonic	HOXA2	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr7	27140743	27140743	C	A	exonic	HOXA2	stopgain	UCEC\|1\|248\|0.00403

Disease information of HOXA2

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
HOXA2	Malignant neoplasm of stomach	C04;C06	Neoplastic Process	CTD_human
HOXA2	Stomach Neoplasms	C04;C06	Neoplastic Process	CTD_human
HOXA2	Congenital small ears	C09;C16	Congenital Abnormality	ORPHANET
HOXA2	Hereditary Diffuse Gastric Cancer	C04;C06	Neoplastic Process	CTD_human
HOXA2	Microtia, Hearing Impairment, And Cleft Palate	C05;C07;C09;C10;C16;C23	Disease or Syndrome	CTD_human;ORPHANET;UNIPROT
HOXA2	MICROTIA WITH OR WITHOUT HEARING IMPAIRMENT		Disease or Syndrome	UNIPROT

Pathway associated with HOXA2

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number

Go term information of HOXA2

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GO_term_name	GO_term_type	TF_name
GO_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT	BP	HOXA2
GO_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT	BP	HOXA2
GO_SKELETAL_SYSTEM_DEVELOPMENT	BP	HOXA2
GO_NEURON_PROJECTION_DEVELOPMENT	BP	HOXA2
GO_EMBRYONIC_VISCEROCRANIUM_MORPHOGENESIS	BP	HOXA2
GO_MOTOR_NEURON_AXON_GUIDANCE	BP	HOXA2
GO_CELLULAR_RESPONSE_TO_RETINOIC_ACID	BP	HOXA2
GO_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION	BP	HOXA2
GO_MIDDLE_EAR_MORPHOGENESIS	BP	HOXA2
GO_CRANIAL_SKELETAL_SYSTEM_DEVELOPMENT	BP	HOXA2
GO_SEGMENT_SPECIFICATION	BP	HOXA2
GO_CELL_FATE_DETERMINATION	BP	HOXA2
GO_REGULATION_OF_OSTEOBLAST_DIFFERENTIATION	BP	HOXA2
GO_CELL_FATE_COMMITMENT	BP	HOXA2
GO_OSTEOBLAST_DEVELOPMENT	BP	HOXA2
GO_SENSORY_ORGAN_MORPHOGENESIS	BP	HOXA2
GO_CELL_MORPHOGENESIS_INVOLVED_IN_NEURON_DIFFERENTIATION	BP	HOXA2
GO_NEGATIVE_REGULATION_OF_OSSIFICATION	BP	HOXA2
GO_NEGATIVE_REGULATION_OF_OSTEOBLAST_DIFFERENTIATION	BP	HOXA2
GO_SKELETAL_SYSTEM_MORPHOGENESIS	BP	HOXA2
GO_EMBRYONIC_CRANIAL_SKELETON_MORPHOGENESIS	BP	HOXA2
GO_TRANSCRIPTIONAL_REPRESSOR_ACTIVITY_RNA_POLYMERASE_II_CORE_PROMOTER_PROXIMAL_REGION_SEQUENCE_SPECIFIC_BINDING	MF	HOXA2

Survival analysis of HOXA2

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 HOXA2

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