Cancer CRCdb

TF information

TF name:	SOX4
TF family:	HMG
Ensembl gene ID:	ENSG00000124766
Ensembl protein ID:	ENSP00000244745
Entrez gene ID:	6659

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

Frequency of SOX4 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_01_022	Cell line	Prostate	C4-2B	0.16666666666667
Sample_02_007	Other	Cervical	cervical-cancer_vector	0.31456953642384
Sample_02_078	Primary cell	Neuroblastoma	low-MYCN-Neuroblastoma-patient-cells	0.25
Sample_02_095	Cell line	Mammary Gland	MDA-MB-468	0.33968871595331
Sample_02_096	Cell line	Mammary Gland	ZR-75-1_1	0.1304347826087
Sample_02_166	Cell line	Mammary Gland	HCC1954_Parental	0.312
Sample_02_182	Cell line	Human melanoma	LOX-IMVI	0.21551724137931
Sample_02_197	Cell line	Stomach	SNU1750	0.22222222222222
Sample_02_220	Cell line	Brain	BE2C_1	0.23076923076923
Sample_02_237	Cell line	Colon	V389	0.12810601877416
Sample_02_241	Cell line	Colon	V456	0.066591422121896
Sample_02_296	Cell line	Neuroblastoma	CLB-BER-Lud	0.10405508798776
Sample_02_299	Cell line	Neuroblastoma	CLB-MA	0.18225419664269
Sample_02_302	Cell line	Neuroblastoma	IMR32	0.21428571428571
Sample_02_304	Cell line	Neuroblastoma	N206	0.09375
Sample_02_307	Cell line	Neuroblastoma	SJNB12	0.11267605633803
Sample_02_308	Cell line	Neuroblastoma	SJNB1	0.125
Sample_02_309	Cell line	Neuroblastoma	SJNB6	0.11374407582938
Sample_02_310	Cell line	Neuroblastoma	SJNB8	0.17627785058978
Sample_02_313	Cell line	Neuroblastoma	SK-N-DZ	0.15830115830116
Sample_02_316	Cell line	Neuroblastoma	CHP212	0.31868131868132
Sample_02_319	Cell line	Neuroblastoma	NB-EBc1	0.13294797687861
Sample_02_338	Cell line	Neuroblastoma	BE2	0.26470588235294
Sample_02_358	Cell line	Colon	LS180	0.3001579778831
Sample_02_395	Cell line	Mammary Gland	BT-549	0.39664335664336

SOX4 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name
Sample_02_302	Neuroblastoma	Cell line	IMR32
Sample_02_313	Neuroblastoma	Cell line	SK-N-DZ

SOX4 distribution in all CRCs

Genomic distribution of SEs associated with SOX4

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Mutation of SOX4

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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 SOX4

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
-	chr6	21595117	21595117	A	G	exonic	SOX4	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21594838	21594838	G	T	exonic	SOX4	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21596111	21596111	A	G	exonic	SOX4	nonsynonymous	BLCA\|1\|396\|0.00253
rs773159471	chr6	21595725	21595725	C	T	exonic	SOX4	synonymous	SKCM\|1\|368\|0.00272
rs771490908	chr6	21596085	21596085	C	T	exonic	SOX4	synonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21595635	21595636	GA	-	exonic	SOX4	frameshift	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21595667	21595667	G	A	exonic	SOX4	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs145209759	chr6	21595968	21595968	C	T	exonic	SOX4	synonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr6	21596018	21596018	C	T	exonic	SOX4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr6	21594792	21594792	G	C	exonic	SOX4	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr6	21594835	21594835	G	T	exonic	SOX4	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr6	21595158	21595158	G	A	exonic	SOX4	synonymous	BLCA\|1\|396\|0.00253,LIHC\|1\|373\|0.00268
-	chr6	21595016	21595016	T	-	exonic	SOX4	frameshift	PCPG\|1\|184\|0.00543
rs145209759	chr6	21595968	21595968	C	G	exonic	SOX4	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr6	21595157	21595157	G	T	exonic	SOX4	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21595042	21595042	C	T	exonic	SOX4	synonymous	UCEC\|1\|248\|0.00403
-	chr6	21595921	21595922	TC	-	exonic	SOX4	frameshift	PAAD\|1\|185\|0.00541
-	chr6	21596066	21596066	T	G	exonic	SOX4	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr6	21595253	21595263	GGGGCGGCCAT	-	exonic	SOX4	frameshift	BLCA\|1\|396\|0.00253,THCA\|1\|504\|0.00198
-	chr6	21595659	21595659	G	T	exonic	SOX4	synonymous	HNSC\|1\|512\|0.00195
-	chr6	21596103	21596103	C	T	exonic	SOX4	synonymous	BLCA\|1\|396\|0.00253
-	chr6	21594926	21594926	C	-	exonic	SOX4	frameshift	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr6	21595992	21595992	C	-	exonic	SOX4	frameshift	SARC\|1\|247\|0.00405
-	chr6	21596142	21596142	G	T	exonic	SOX4	synonymous	LUAD\|1\|543\|0.00184
-	chr6	21595085	21595085	C	T	exonic	SOX4	nonsynonymous	GBM\|1\|290\|0.00345,GBMLGG\|1\|820\|0.00122
-	chr6	21595094	21595094	G	C	exonic	SOX4	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr6	21594936	21594936	G	T	exonic	SOX4	synonymous	BRCA\|1\|982\|0.00102
-	chr6	21595211	21595211	C	T	exonic	SOX4	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr6	21595027	21595027	G	A	exonic	SOX4	nonsynonymous	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr6	21595973	21595973	-	GAC	exonic	SOX4	nonframeshift	THYM\|1\|123\|0.00813
-	chr6	21596141	21596141	C	G	exonic	SOX4	nonsynonymous	BLCA\|1\|396\|0.00253,UCS\|1\|57\|0.01754
-	chr6	21595096	21595096	G	A	exonic	SOX4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr6	21595064	21595064	T	G	exonic	SOX4	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr6	21595158	21595158	G	T	exonic	SOX4	nonsynonymous	BLCA\|1\|396\|0.00253
rs564094826	chr6	21595266	21595266	-	GC	exonic	SOX4	frameshift	LUAD\|1\|543\|0.00184,PCPG\|1\|184\|0.00543,THCA\|1\|504\|0.00198
-	chr6	21595268	21595269	GC	-	exonic	SOX4	frameshift	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189,SKCM\|1\|368\|0.00272
-	chr6	21594934	21594934	G	-	exonic	SOX4	frameshift	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189

Disease information of SOX4

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
SOX4	Adenoid Cystic Carcinoma	C04	Neoplastic Process	CTD_human
SOX4	Hepatoma, Morris	C04;C06	Experimental Model of Disease; Neoplastic Process	CTD_human
SOX4	Hepatoma, Novikoff	C04;C06	Experimental Model of Disease; Neoplastic Process	CTD_human
SOX4	Liver Cirrhosis, Experimental	C06	Experimental Model of Disease	CTD_human
SOX4	Liver Neoplasms, Experimental	C04;C06	Experimental Model of Disease; Neoplastic Process	CTD_human
SOX4	Salivary Gland Neoplasms	C04;C07	Neoplastic Process	CTD_human
SOX4	Experimental Hepatoma	C04;C06	Experimental Model of Disease; Neoplastic Process	CTD_human
SOX4	Malignant neoplasm of salivary gland	C04;C07	Neoplastic Process	CTD_human

Pathway associated with SOX4

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number
pathway0000549	Deactivation of the beta-catenin transactivating complex	reactome	42	236

Go term information of SOX4

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GO_term_name	GO_term_type	TF_name
GO_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION	BP	SOX4
GO_SOMATIC_STEM_CELL_POPULATION_MAINTENANCE	BP	SOX4
GO_CARDIAC_SEPTUM_DEVELOPMENT	BP	SOX4
GO_VENTRICULAR_SEPTUM_MORPHOGENESIS	BP	SOX4
GO_CARDIAC_CHAMBER_MORPHOGENESIS	BP	SOX4
GO_REGULATION_OF_PROTEIN_EXPORT_FROM_NUCLEUS	BP	SOX4
GO_MORPHOGENESIS_OF_EMBRYONIC_EPITHELIUM	BP	SOX4
GO_CELL_DIFFERENTIATION_IN_SPINAL_CORD	BP	SOX4
GO_SPINAL_CORD_MOTOR_NEURON_DIFFERENTIATION	BP	SOX4
GO_PANCREAS_DEVELOPMENT	BP	SOX4
GO_AORTA_DEVELOPMENT	BP	SOX4
GO_VENTRAL_SPINAL_CORD_DEVELOPMENT	BP	SOX4
GO_CELL_CELL_ADHESION	BP	SOX4
GO_POSITIVE_REGULATION_OF_INSULIN_SECRETION	BP	SOX4
GO_NEGATIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT	BP	SOX4
GO_CARDIAC_ATRIUM_DEVELOPMENT	BP	SOX4
GO_ATRIAL_SEPTUM_DEVELOPMENT	BP	SOX4
GO_ARTERY_MORPHOGENESIS	BP	SOX4
GO_ATRIAL_SEPTUM_MORPHOGENESIS	BP	SOX4
GO_SIGNAL_TRANSDUCTION_IN_RESPONSE_TO_DNA_DAMAGE	BP	SOX4
GO_CANONICAL_WNT_SIGNALING_PATHWAY	BP	SOX4
GO_GLIOGENESIS	BP	SOX4
GO_ENDOCRINE_PANCREAS_DEVELOPMENT	BP	SOX4
GO_G1_DNA_DAMAGE_CHECKPOINT	BP	SOX4
GO_NEGATIVE_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION	BP	SOX4
GO_CARDIAC_VENTRICLE_MORPHOGENESIS	BP	SOX4
GO_PROTEIN_STABILIZATION	BP	SOX4
GO_CARDIAC_RIGHT_VENTRICLE_MORPHOGENESIS	BP	SOX4
GO_SYMPATHETIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	SOX4
GO_POSITIVE_REGULATION_OF_HORMONE_SECRETION	BP	SOX4
GO_TUBE_DEVELOPMENT	BP	SOX4
GO_MITOTIC_DNA_INTEGRITY_CHECKPOINT	BP	SOX4
GO_REGULATION_OF_PROTEIN_ACETYLATION	BP	SOX4
GO_REGULATION_OF_PROTEIN_STABILITY	BP	SOX4
GO_MITOTIC_CELL_CYCLE_CHECKPOINT	BP	SOX4
GO_VENTRICULAR_SEPTUM_DEVELOPMENT	BP	SOX4
GO_COLUMNAR_CUBOIDAL_EPITHELIAL_CELL_DIFFERENTIATION	BP	SOX4
GO_POSITIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY	BP	SOX4
GO_NEGATIVE_REGULATION_OF_CELL_CYCLE_PHASE_TRANSITION	BP	SOX4
GO_POSITIVE_REGULATION_OF_PROTEIN_ACETYLATION	BP	SOX4
GO_HEART_VALVE_DEVELOPMENT	BP	SOX4
GO_NEGATIVE_REGULATION_OF_CELL_CYCLE_G1_S_PHASE_TRANSITION	BP	SOX4
GO_REGULATION_OF_CELLULAR_AMIDE_METABOLIC_PROCESS	BP	SOX4
GO_POSITIVE_REGULATION_OF_PROTEIN_MODIFICATION_PROCESS	BP	SOX4
GO_REGULATION_OF_CELL_DEATH	BP	SOX4
GO_AUTONOMIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	SOX4
GO_NEUROEPITHELIAL_CELL_DIFFERENTIATION	BP	SOX4
GO_REGULATION_OF_PROTEIN_MODIFICATION_PROCESS	BP	SOX4
GO_CARDIAC_CHAMBER_FORMATION	BP	SOX4
GO_KIDNEY_MORPHOGENESIS	BP	SOX4
GO_DNA_DAMAGE_RESPONSE_DETECTION_OF_DNA_DAMAGE	BP	SOX4
GO_CARDIAC_SEPTUM_MORPHOGENESIS	BP	SOX4
GO_CELL_CYCLE_CHECKPOINT	BP	SOX4
GO_ATRIOVENTRICULAR_VALVE_DEVELOPMENT	BP	SOX4
GO_LYMPHOID_PROGENITOR_CELL_DIFFERENTIATION	BP	SOX4
GO_ATRIOVENTRICULAR_VALVE_MORPHOGENESIS	BP	SOX4
GO_AORTA_MORPHOGENESIS	BP	SOX4
GO_POSITIVE_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION	BP	SOX4
GO_CORE_PROMOTER_BINDING	MF	SOX4
GO_TRANSCRIPTIONAL_ACTIVATOR_ACTIVITY_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_BINDING	MF	SOX4
GO_TRANSCRIPTIONAL_REPRESSOR_ACTIVITY_RNA_POLYMERASE_II_ACTIVATING_TRANSCRIPTION_FACTOR_BINDING	MF	SOX4
GO_RNA_POLYMERASE_II_TRANSCRIPTION_COACTIVATOR_ACTIVITY	MF	SOX4
GO_CORE_PROMOTER_SEQUENCE_SPECIFIC_DNA_BINDING	MF	SOX4

Survival analysis of SOX4

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 SOX4

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