Cancer CRCdb

TF information

TF name:	SIX3
TF family:	Homeobox
Ensembl gene ID:	ENSG00000138083
Ensembl protein ID:	ENSP00000260653
Entrez gene ID:	6496

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

Frequency of SIX3 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_296	Cell line	Neuroblastoma	CLB-BER-Lud	0.0061208875286917
Sample_02_300	Cell line	Neuroblastoma	CLB-PE	0.051282051282051
Sample_02_302	Cell line	Neuroblastoma	IMR32	0.035714285714286
Sample_02_303	Cell line	Neuroblastoma	LAN1	0.057142857142857
Sample_02_312	Cell line	Neuroblastoma	SK-N-BE_2-C	0.042553191489362
Sample_02_313	Cell line	Neuroblastoma	SK-N-DZ	0.023166023166023
Sample_02_314	Cell line	Neuroblastoma	SK-N-FI	0.012345679012346
Sample_02_318	Cell line	Neuroblastoma	NB69	0.046875
Sample_02_319	Cell line	Neuroblastoma	NB-EBc1	0.011560693641618

SIX3 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name

SIX3 distribution in all CRCs

Genomic distribution of SEs associated with SIX3

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Mutation of SIX3

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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 SIX3

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
-	chr2	45169343	45169343	G	C	exonic	SIX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr2	45169367	45169367	G	C	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45170024	45170024	G	T	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45170028	45170028	G	A	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169584	45169584	C	T	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45171841	45171841	C	T	exonic	SIX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr2	45169558	45169558	C	G	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45169936	45169936	C	A	exonic	SIX3	synonymous	LUAD\|1\|543\|0.00184
rs753721024	chr2	45169340	45169340	G	A	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169642	45169642	C	A	exonic	SIX3	synonymous	CESC\|1\|194\|0.00515
-	chr2	45169312	45169312	C	T	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs746508020	chr2	45169610	45169610	G	A	exonic	SIX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr2	45171878	45171878	C	G	exonic	SIX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr2	45169609	45169609	C	T	exonic	SIX3	synonymous	PAAD\|1\|185\|0.00541,STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169453	45169453	C	T	exonic	SIX3	synonymous	HNSC\|1\|512\|0.00195
-	chr2	45169645	45169645	G	A	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169257	45169257	C	-	exonic	SIX3	frameshift	ESCA\|1\|185\|0.00541
-	chr2	45169549	45169549	G	T	exonic	SIX3	synonymous	LUAD\|1\|543\|0.00184
-	chr2	45170038	45170038	G	A	exonic	SIX3	synonymous	SKCM\|2\|368\|0.00543
-	chr2	45169910	45169910	G	C	exonic	SIX3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr2	45169648	45169648	C	T	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169617	45169617	T	C	exonic	SIX3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr2	45170049	45170049	G	T	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45171737	45171737	C	A	exonic	SIX3	synonymous	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr2	45171797	45171797	G	A	exonic	SIX3	synonymous	ESCA\|1\|185\|0.00541,LIHC\|1\|373\|0.00268
-	chr2	45169460	45169460	C	T	exonic	SIX3	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr2	45169387	45169387	C	T	exonic	SIX3	synonymous	ESCA\|1\|185\|0.00541
-	chr2	45170030	45170030	G	A	exonic	SIX3	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr2	45169477	45169477	C	T	exonic	SIX3	synonymous	SKCM\|1\|368\|0.00272
-	chr2	45169254	45169254	G	A	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45169961	45169961	G	T	exonic	SIX3	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr2	45171770	45171770	G	A	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169750	45169750	G	A	exonic	SIX3	stopgain	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169640	45169640	C	-	exonic	SIX3	frameshift	ESCA\|1\|185\|0.00541,STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169338	45169338	G	A	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr2	45169813	45169813	G	A	exonic	SIX3	synonymous	UCEC\|1\|248\|0.00403
-	chr2	45169910	45169910	G	T	exonic	SIX3	stopgain	BRCA\|2\|982\|0.00204
rs777810054	chr2	45169356	45169356	C	T	exonic	SIX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs338074	chr2	45171842	45171842	A	G	exonic	SIX3	synonymous	ACC\|6\|90\|0.06667
-	chr2	45169769	45169769	G	A	exonic	SIX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr2	45169576	45169576	C	T	exonic	SIX3	synonymous	HNSC\|1\|512\|0.00195
-	chr2	45171872	45171872	C	T	exonic	SIX3	synonymous	ESCA\|1\|185\|0.00541
-	chr2	45169727	45169727	C	T	exonic	SIX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr2	45169423	45169423	C	T	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs746201264	chr2	45169459	45169459	C	T	exonic	SIX3	synonymous	HNSC\|1\|512\|0.00195
-	chr2	45169297	45169297	C	A	exonic	SIX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr2	45169510	45169510	G	A	exonic	SIX3	synonymous	HNSC\|1\|512\|0.00195
rs202214767	chr2	45169339	45169339	C	T	exonic	SIX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs763853335	chr2	45169458	45169458	C	-	exonic	SIX3	frameshift	STAD\|2\|395\|0.00506,STES\|2\|395\|0.00506
rs753054738	chr2	45169955	45169955	G	A	exonic	SIX3	nonsynonymous	SKCM\|2\|368\|0.00543
rs759831587	chr2	45169954	45169954	C	T	exonic	SIX3	synonymous	LUAD\|1\|543\|0.00184
-	chr2	45169427	45169427	G	T	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45169361	45169361	G	T	exonic	SIX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr2	45171798	45171798	G	A	exonic	SIX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr2	45169636	45169636	C	T	exonic	SIX3	synonymous	CESC\|1\|194\|0.00515
-	chr2	45169292	45169292	C	A	exonic	SIX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr2	45171842	45171842	A	-	exonic	SIX3	frameshift	LUAD\|3\|543\|0.00552
-	chr2	45169644	45169644	C	T	exonic	SIX3	nonsynonymous	PAAD\|1\|185\|0.00541
-	chr2	45169256	45169256	-	C	exonic	SIX3	frameshift	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222

Disease information of SIX3

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
SIX3	Congenital ocular coloboma (disorder)	C11;C16	Congenital Abnormality	GENOMICS_ENGLAND
SIX3	Liver neoplasms	C04;C06	Neoplastic Process	CTD_human
SIX3	Precancerous Conditions	C04	Neoplastic Process	CTD_human
SIX3	Arhinencephaly	C05;C10;C16	Congenital Abnormality	CTD_human
SIX3	Holoprosencephaly	C05;C10;C16	Congenital Abnormality	CTD_human;GENOMICS_ENGLAND
SIX3	Cataract	C11	Acquired Abnormality	GENOMICS_ENGLAND
SIX3	Schizencephaly	C10;C16	Congenital Abnormality	ORPHANET;UNIPROT
SIX3	Condition, Preneoplastic	C04	Neoplastic Process	CTD_human
SIX3	Malignant neoplasm of liver	C04;C06	Neoplastic Process	CTD_human
SIX3	Lobar Holoprosencephaly	C05;C10;C16	Congenital Abnormality	CTD_human;ORPHANET
SIX3	Alobar Holoprosencephaly	C05;C10;C16	Congenital Abnormality	CTD_human;ORPHANET
SIX3	Epileptic encephalopathy		Disease or Syndrome	GENOMICS_ENGLAND
SIX3	Semilobar Holoprosencephaly	C05;C10;C16	Congenital Abnormality	CTD_human;ORPHANET
SIX3	HOLOPROSENCEPHALY 2 (disorder)	C05;C10;C16	Disease or Syndrome	CTD_human;UNIPROT
SIX3	Familial schizencephaly	C10;C16	Disease or Syndrome	CTD_human
SIX3	Intellectual Disability	C10;C23;F01;F03	Mental or Behavioral Dysfunction	GENOMICS_ENGLAND

Pathway associated with SIX3

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number

Go term information of SIX3

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GO_term_name	GO_term_type	TF_name
GO_CIRCADIAN_RHYTHM	BP	SIX3
GO_LENS_FIBER_CELL_DIFFERENTIATION	BP	SIX3
GO_AXIS_SPECIFICATION	BP	SIX3
GO_PITUITARY_GLAND_DEVELOPMENT	BP	SIX3
GO_DEVELOPMENTAL_INDUCTION	BP	SIX3
GO_CELL_PROLIFERATION_IN_FOREBRAIN	BP	SIX3
GO_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT	BP	SIX3
GO_DORSAL_VENTRAL_PATTERN_FORMATION	BP	SIX3
GO_FOREBRAIN_REGIONALIZATION	BP	SIX3
GO_PROXIMAL_DISTAL_PATTERN_FORMATION	BP	SIX3
GO_PROTEIN_IMPORT_INTO_NUCLEUS_TRANSLOCATION	BP	SIX3
GO_EMBRYONIC_CAMERA_TYPE_EYE_MORPHOGENESIS	BP	SIX3
GO_REGULATION_OF_NEUROBLAST_PROLIFERATION	BP	SIX3
GO_APOPTOTIC_PROCESS_INVOLVED_IN_DEVELOPMENT	BP	SIX3
GO_EPITHELIAL_CELL_APOPTOTIC_PROCESS	BP	SIX3
GO_HEAD_DEVELOPMENT	BP	SIX3
GO_RHYTHMIC_BEHAVIOR	BP	SIX3
GO_DIENCEPHALON_DEVELOPMENT	BP	SIX3
GO_EMBRYONIC_EYE_MORPHOGENESIS	BP	SIX3
GO_TELENCEPHALON_REGIONALIZATION	BP	SIX3
GO_LENS_MORPHOGENESIS_IN_CAMERA_TYPE_EYE	BP	SIX3
GO_NEGATIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY	BP	SIX3
GO_REGULATION_OF_NEURAL_PRECURSOR_CELL_PROLIFERATION	BP	SIX3
GO_EPITHELIAL_CELL_MATURATION	BP	SIX3
GO_REGULATION_OF_CELL_DEVELOPMENT	BP	SIX3
GO_REGIONALIZATION	BP	SIX3
GO_EMBRYONIC_CAMERA_TYPE_EYE_DEVELOPMENT	BP	SIX3
GO_LENS_DEVELOPMENT_IN_CAMERA_TYPE_EYE	BP	SIX3
GO_TRANSCRIPTIONAL_ACTIVATOR_ACTIVITY_RNA_POLYMERASE_II_DISTAL_ENHANCER_SEQUENCE_SPECIFIC_BINDING	MF	SIX3
GO_TRANSCRIPTION_FACTOR_ACTIVITY_RNA_POLYMERASE_II_DISTAL_ENHANCER_SEQUENCE_SPECIFIC_BINDING	MF	SIX3
GO_TRANSCRIPTION_COFACTOR_BINDING	MF	SIX3
GO_TRANSCRIPTION_COACTIVATOR_ACTIVITY	MF	SIX3
GO_RNA_POLYMERASE_II_DISTAL_ENHANCER_SEQUENCE_SPECIFIC_DNA_BINDING	MF	SIX3

Survival analysis of SIX3

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 SIX3

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