Cancer CRCdb

TF information

TF name:	RFX3
TF family:	RFX
Ensembl gene ID:	ENSG00000080298
Ensembl protein ID:	ENSP00000351574, ENSP00000482598, ENSP00000303847, ENSP00000405664, ENSP00000371434
Entrez gene ID:	5991

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

Frequency of RFX3 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_114	Cell line	Mammary Gland	CAL51	0.28643216080402
Sample_02_161	Cell line	Brain	U87	0.4
Sample_02_180	Cell line	Human melanoma	CJM	0.171875
Sample_02_182	Cell line	Human melanoma	LOX-IMVI	0.068965517241379
Sample_02_309	Cell line	Neuroblastoma	SJNB6	0.4739336492891
Sample_02_310	Cell line	Neuroblastoma	SJNB8	0.17496723460026
Sample_02_314	Cell line	Neuroblastoma	SK-N-FI	0.33333333333333

RFX3 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name
Sample_02_161	Brain	Cell line	U87
Sample_02_309	Neuroblastoma	Cell line	SJNB6

RFX3 distribution in all CRCs

Genomic distribution of SEs associated with RFX3

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Mutation of RFX3

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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 RFX3

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
rs769875021	chr9	3247895	3247895	A	G	exonic	RFX3	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr9	3257056	3257056	G	T	exonic	RFX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3275580	3275580	C	A	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3266285	3266285	G	A	exonic	RFX3	stopgain	SKCM\|1\|368\|0.00272
-	chr9	3270522	3270522	A	T	exonic	RFX3	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr9	3263055	3263055	A	C	exonic	RFX3	synonymous	ACC\|1\|90\|0.01111
-	chr9	3248157	3248157	G	A	exonic	RFX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3225231	3225231	A	-	exonic	RFX3	frameshift	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr9	3263044	3263044	T	C	exonic	RFX3	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr9	3330346	3330346	G	T	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3257050	3257050	T	A	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3247911	3247911	T	C	exonic	RFX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr9	3263051	3263051	G	A	exonic	RFX3	stopgain	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204,HNSC\|1\|512\|0.00195
-	chr9	3247939	3247939	C	T	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3330369	3330369	C	T	exonic	RFX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs757220727	chr9	3225114	3225114	G	A	exonic	RFX3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3293119	3293119	C	T	exonic	RFX3	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr9	3266284	3266284	C	T	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3262957	3262957	C	T	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204,STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3248121	3248121	G	A	exonic	RFX3	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr9	3277390	3277390	G	C	exonic	RFX3	nonsynonymous	CESC\|1\|194\|0.00515
rs865829359	chr9	3263030	3263030	G	A	exonic	RFX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr9	3293233	3293233	T	C	exonic	RFX3	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr9	3271084	3271084	C	G	exonic	RFX3	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr9	3257113	3257113	G	A	exonic	RFX3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs753950808	chr9	3275558	3275558	T	C	exonic	RFX3	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr9	3270497	3270497	G	T	exonic	RFX3	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr9	3330465	3330465	C	A	exonic	RFX3	stopgain	SKCM\|1\|368\|0.00272
-	chr9	3225279	3225279	A	T	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3346710	3346710	G	A	exonic	RFX3	stopgain	LIHC\|1\|373\|0.00268
-	chr9	3248113	3248113	G	C	exonic	RFX3	synonymous	BLCA\|1\|396\|0.00253
-	chr9	3275524	3275524	C	G	exonic	RFX3	nonsynonymous	CESC\|1\|194\|0.00515
-	chr9	3271067	3271067	A	C	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3248153	3248153	C	T	exonic	RFX3	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr9	3257180	3257180	C	T	exonic	RFX3	nonsynonymous	SARC\|1\|247\|0.00405
-	chr9	3266222	3266222	T	C	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3330439	3330439	C	T	exonic	RFX3	synonymous	HNSC\|1\|512\|0.00195
-	chr9	3301560	3301560	G	A	exonic	RFX3	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr9	3270456	3270456	G	A	exonic	RFX3	synonymous	SKCM\|1\|368\|0.00272
-	chr9	3330347	3330347	C	T	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3263047	3263047	C	G	exonic	RFX3	nonsynonymous	OV\|1\|469\|0.00213
-	chr9	3346697	3346697	C	T	exonic	RFX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr9	3346745	3346745	A	-	exonic	RFX3	frameshift	BRCA\|1\|982\|0.00102
-	chr9	3248068	3248068	C	T	exonic	RFX3	synonymous	LUAD\|1\|543\|0.00184
-	chr9	3330299	3330299	C	T	exonic	RFX3	nonsynonymous	BLCA\|2\|396\|0.00505
-	chr9	3270405	3270405	C	A	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3293151	3293151	T	C	exonic	RFX3	synonymous	UCEC\|1\|248\|0.00403
rs374087462	chr9	3225083	3225083	T	C	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3301594	3301594	T	A	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3275593	3275593	T	C	exonic	RFX3	synonymous	CESC\|1\|194\|0.00515
-	chr9	3293110	3293110	A	C	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3247980	3247980	C	A	exonic	RFX3	stopgain	UCEC\|1\|248\|0.00403
-	chr9	3275520	3275520	G	C	exonic	RFX3	nonsynonymous	HNSC\|1\|512\|0.00195
rs137899630	chr9	3225104	3225104	C	T	exonic	RFX3	nonsynonymous	GBM\|1\|290\|0.00345,GBMLGG\|1\|820\|0.00122
-	chr9	3266289	3266289	G	A	exonic	RFX3	synonymous	ESCA\|1\|185\|0.00541
-	chr9	3293120	3293120	T	G	exonic	RFX3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3277363	3277363	C	T	exonic	RFX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr9	3330272	3330272	G	A	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3330293	3330293	G	A	exonic	RFX3	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr9	3330276	3330276	G	A	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3247930	3247930	G	T	exonic	RFX3	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr9	3270426	3270426	C	A	exonic	RFX3	synonymous	LUAD\|1\|543\|0.00184
-	chr9	3277378	3277378	G	A	exonic	RFX3	nonsynonymous	CESC\|1\|194\|0.00515
-	chr9	3262980	3262980	G	T	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3346738	3346738	C	T	exonic	RFX3	synonymous	SKCM\|1\|368\|0.00272
-	chr9	3271010	3271010	C	T	exonic	RFX3	nonsynonymous	LAML\|1\|197\|0.00508
-	chr9	3293163	3293163	G	T	exonic	RFX3	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr9	3270516	3270516	A	C	exonic	RFX3	nonsynonymous	LUSC\|1\|178\|0.00562
rs113424988	chr9	3225156	3225156	G	A	exonic	RFX3	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3248069	3248069	T	C	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3293175	3293175	G	A	exonic	RFX3	synonymous	PRAD\|1\|499\|0.00200
-	chr9	3263012	3263012	G	C	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3225259	3225259	C	T	exonic	RFX3	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr9	3263041	3263041	G	T	exonic	RFX3	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr9	3225181	3225181	G	A	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3270393	3270393	G	T	exonic	RFX3	synonymous	ESCA\|1\|185\|0.00541
-	chr9	3225132	3225132	G	A	exonic	RFX3	synonymous	OV\|1\|469\|0.00213
-	chr9	3293227	3293227	G	C	exonic	RFX3	nonsynonymous	BRCA\|1\|982\|0.00102
rs540836639	chr9	3330319	3330319	G	T	exonic	RFX3	synonymous	ESCA\|1\|185\|0.00541
rs764392006	chr9	3330445	3330445	A	C	exonic	RFX3	synonymous	UCEC\|1\|248\|0.00403
-	chr9	3263080	3263080	G	A	exonic	RFX3	nonsynonymous	PCPG\|1\|184\|0.00543
-	chr9	3263050	3263050	C	T	exonic	RFX3	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr9	3275553	3275553	T	C	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3270389	3270389	C	T	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3271119	3271119	C	T	splicing	RFX3	splicing	SKCM\|1\|368\|0.00272
-	chr9	3395586	3395586	C	G	exonic	RFX3	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr9	3277416	3277416	T	G	exonic	RFX3	synonymous	LUSC\|1\|178\|0.00562
-	chr9	3257078	3257078	A	G	exonic	RFX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3248100	3248100	T	-	exonic	RFX3	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3248151	3248151	C	T	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
rs370801268	chr9	3330481	3330481	C	T	exonic	RFX3	nonsynonymous	OV\|1\|469\|0.00213
-	chr9	3288164	3288164	G	A	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr9	3270471	3270471	G	A	exonic	RFX3	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3225139	3225139	G	C	exonic	RFX3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr9	3257179	3257179	G	A	exonic	RFX3	synonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr9	3277341	3277341	-	A	exonic	RFX3	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3263017	3263017	G	T	exonic	RFX3	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr9	3293131	3293131	C	A	exonic	RFX3	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr9	3247979	3247979	T	A	exonic	RFX3	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr9	3257077	3257077	C	A	exonic	RFX3	synonymous	LUAD\|1\|543\|0.00184
-	chr9	3247924	3247924	G	A	exonic	RFX3	synonymous	LUAD\|1\|543\|0.00184
-	chr9	3330515	3330515	C	A	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3257090	3257090	C	T	exonic	RFX3	stopgain	BLCA\|1\|396\|0.00253
-	chr9	3346746	3346746	-	A	exonic	RFX3	frameshift	BRCA\|2\|982\|0.00204
rs766962228	chr9	3266248	3266248	T	C	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3225217	3225217	G	C	exonic	RFX3	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr9	3330483	3330483	T	C	exonic	RFX3	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr9	3293098	3293098	C	T	exonic	RFX3	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr9	3288251	3288251	C	G	splicing	RFX3	splicing	BLCA\|1\|396\|0.00253
-	chr9	3271027	3271027	T	C	exonic	RFX3	nonsynonymous	PAAD\|1\|185\|0.00541
-	chr9	3288187	3288187	C	A	exonic	RFX3	synonymous	LUAD\|1\|543\|0.00184
-	chr9	3271070	3271070	A	T	exonic	RFX3	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr9	3293183	3293183	G	A	exonic	RFX3	nonsynonymous	SKCM\|1\|368\|0.00272
rs757346391	chr9	3301562	3301562	G	C	exonic	RFX3	nonsynonymous	OV\|1\|469\|0.00213
rs757761534	chr9	3225066	3225066	T	C	exonic	RFX3	synonymous	BRCA\|1\|982\|0.00102
-	chr9	3225258	3225258	A	C	exonic	RFX3	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr9	3330505	3330505	C	A	exonic	RFX3	synonymous	LUSC\|1\|178\|0.00562
-	chr9	3247999	3247999	C	A	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3275544	3275544	C	T	exonic	RFX3	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr9	3228886	3228886	C	T	exonic	RFX3	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr9	3346722	3346722	G	A	exonic	RFX3	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr9	3257090	3257090	C	A	exonic	RFX3	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr9	3248085	3248085	C	A	exonic	RFX3	stopgain	ESCA\|1\|185\|0.00541
rs757065522	chr9	3293099	3293099	G	A	exonic	RFX3	stopgain	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253

Disease information of RFX3

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
RFX3	Dermatologic disorders	C17	Disease or Syndrome	CTD_human
RFX3	Arsenic Poisoning, Inorganic	C10;C25	Injury or Poisoning	CTD_human
RFX3	Nervous System, Organic Arsenic Poisoning	C10;C25	Injury or Poisoning	CTD_human
RFX3	Arsenic Poisoning	C10;C25	Injury or Poisoning	CTD_human
RFX3	Arsenic Encephalopathy	C10;C25	Disease or Syndrome	CTD_human
RFX3	Arsenic Induced Polyneuropathy	C10;C25	Injury or Poisoning	CTD_human

Pathway associated with RFX3

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number

Go term information of RFX3

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GO_term_name	GO_term_type	TF_name
GO_NEGATIVE_REGULATION_OF_GENE_EXPRESSION	BP	RFX3
GO_TYPE_B_PANCREATIC_CELL_DEVELOPMENT	BP	RFX3
GO_POSITIVE_REGULATION_OF_BIOSYNTHETIC_PROCESS	BP	RFX3
GO_PANCREAS_DEVELOPMENT	BP	RFX3
GO_GLANDULAR_EPITHELIAL_CELL_DEVELOPMENT	BP	RFX3
GO_EPITHELIAL_CILIUM_MOVEMENT	BP	RFX3
GO_REGULATION_OF_PROTEIN_SECRETION	BP	RFX3
GO_ENDOCRINE_PANCREAS_DEVELOPMENT	BP	RFX3
GO_CILIUM_ORGANIZATION	BP	RFX3
GO_CILIUM_MOVEMENT	BP	RFX3
GO_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY	BP	RFX3
GO_ORGANELLE_ASSEMBLY	BP	RFX3
GO_COLUMNAR_CUBOIDAL_EPITHELIAL_CELL_DEVELOPMENT	BP	RFX3
GO_REGULATION_OF_PROTEIN_LOCALIZATION	BP	RFX3
GO_COLUMNAR_CUBOIDAL_EPITHELIAL_CELL_DIFFERENTIATION	BP	RFX3
GO_ENTEROENDOCRINE_CELL_DIFFERENTIATION	BP	RFX3
GO_CELLULAR_COMPONENT_MORPHOGENESIS	BP	RFX3
GO_REGULATION_OF_PEPTIDE_SECRETION	BP	RFX3
GO_REGULATION_OF_TRANSPORT	BP	RFX3
GO_EPITHELIAL_CELL_MATURATION	BP	RFX3
GO_GLANDULAR_EPITHELIAL_CELL_DIFFERENTIATION	BP	RFX3
GO_TRANSCRIPTION_FACTOR_ACTIVITY_RNA_POLYMERASE_II_DISTAL_ENHANCER_SEQUENCE_SPECIFIC_BINDING	MF	RFX3

Survival analysis of RFX3

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 RFX3

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