Cancer CRCdb

TF information

TF name:	PHOX2B
TF family:	Homeobox
Ensembl gene ID:	ENSG00000109132
Ensembl protein ID:	ENSP00000226382
Entrez gene ID:	8929

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

Frequency of PHOX2B in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_078	Primary cell	Neuroblastoma	low-MYCN-Neuroblastoma-patient-cells	0.5
Sample_02_254	Cell line	Neuroblastoma	IMR5-75	0.47058823529412
Sample_02_296	Cell line	Neuroblastoma	CLB-BER-Lud	0.30374904361132
Sample_02_298	Cell line	Neuroblastoma	CLB-GA	0.91780821917808
Sample_02_299	Cell line	Neuroblastoma	CLB-MA	0.28776978417266
Sample_02_300	Cell line	Neuroblastoma	CLB-PE	0.47435897435897
Sample_02_303	Cell line	Neuroblastoma	LAN1	0.94285714285714
Sample_02_304	Cell line	Neuroblastoma	N206	0.36820652173913
Sample_02_307	Cell line	Neuroblastoma	SJNB12	0.40845070422535
Sample_02_308	Cell line	Neuroblastoma	SJNB1	0.546875
Sample_02_309	Cell line	Neuroblastoma	SJNB6	0.3175355450237
Sample_02_310	Cell line	Neuroblastoma	SJNB8	0.44167758846658
Sample_02_311	Cell line	Neuroblastoma	SK-N-AS	0.71428571428571
Sample_02_312	Cell line	Neuroblastoma	SK-N-BE_2-C	0.6063829787234
Sample_02_313	Cell line	Neuroblastoma	SK-N-DZ	0.45173745173745
Sample_02_314	Cell line	Neuroblastoma	SK-N-FI	0.66049382716049
Sample_02_316	Cell line	Neuroblastoma	CHP212	0.21428571428571
Sample_02_318	Cell line	Neuroblastoma	NB69	0.7265625
Sample_02_319	Cell line	Neuroblastoma	NB-EBc1	0.58381502890173

PHOX2B distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name
Sample_02_078	Neuroblastoma	Primary cell	low-MYCN-Neuroblastoma-patient-cells
Sample_02_254	Neuroblastoma	Cell line	IMR5-75
Sample_02_298	Neuroblastoma	Cell line	CLB-GA
Sample_02_299	Neuroblastoma	Cell line	CLB-MA
Sample_02_300	Neuroblastoma	Cell line	CLB-PE
Sample_02_303	Neuroblastoma	Cell line	LAN1
Sample_02_307	Neuroblastoma	Cell line	SJNB12
Sample_02_308	Neuroblastoma	Cell line	SJNB1
Sample_02_310	Neuroblastoma	Cell line	SJNB8
Sample_02_311	Neuroblastoma	Cell line	SK-N-AS
Sample_02_312	Neuroblastoma	Cell line	SK-N-BE_2-C
Sample_02_314	Neuroblastoma	Cell line	SK-N-FI
Sample_02_318	Neuroblastoma	Cell line	NB69
Sample_02_319	Neuroblastoma	Cell line	NB-EBc1

PHOX2B distribution in all CRCs

Genomic distribution of SEs associated with PHOX2B

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Mutation of PHOX2B

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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 PHOX2B

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
-	chr4	41747890	41747890	G	T	exonic	PHOX2B	nonsynonymous	TGCT\|1\|155\|0.00645
rs749994532	chr4	41749528	41749528	G	A	exonic	PHOX2B	synonymous	HNSC\|1\|512\|0.00195
-	chr4	41748256	41748256	G	T	exonic	PHOX2B	synonymous	UCEC\|1\|248\|0.00403
-	chr4	41750565	41750565	C	T	exonic	PHOX2B	nonsynonymous	SKCM\|2\|368\|0.00543
-	chr4	41750617	41750617	A	C	exonic	PHOX2B	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr4	41750553	41750553	G	A	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
rs748614674	chr4	41749404	41749404	G	C	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41748145	41748145	G	A	exonic	PHOX2B	synonymous	UCEC\|1\|248\|0.00403
-	chr4	41749702	41749702	G	T	intronic	PHOX2B	unknown	UCEC\|1\|248\|0.00403
-	chr4	41750600	41750600	T	C	exonic	PHOX2B	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr4	41748082	41748082	G	A	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
-	chr4	41747994	41748013	CCGCCGCTGCCGCTGCCGCC	-	exonic	PHOX2B	frameshift	BLCA\|1\|396\|0.00253,HNSC\|1\|512\|0.00195,PAAD\|1\|185\|0.00541
-	chr4	41748110	41748110	G	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41750440	41750440	C	-	exonic	PHOX2B	frameshift	LUAD\|1\|543\|0.00184
rs147497096	chr4	41749390	41749390	G	A	exonic	PHOX2B	synonymous	HNSC\|1\|512\|0.00195
-	chr4	41747907	41747907	C	T	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41749465	41749465	G	T	exonic	PHOX2B	synonymous	UCEC\|1\|248\|0.00403
rs73810366	chr4	41750394	41750394	G	A	exonic	PHOX2B	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41747863	41747863	G	C	exonic	PHOX2B	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr4	41749533	41749533	C	A	exonic	PHOX2B	nonsynonymous	ESCA\|1\|185\|0.00541
-	chr4	41747866	41747866	G	T	exonic	PHOX2B	synonymous	BLCA\|1\|396\|0.00253
-	chr4	41748245	41748245	T	-	exonic	PHOX2B	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41749461	41749461	C	G	exonic	PHOX2B	nonsynonymous	OV\|1\|469\|0.00213
-	chr4	41750451	41750451	G	A	exonic	PHOX2B	synonymous	SKCM\|2\|368\|0.00543
-	chr4	41748274	41748274	G	A	exonic	PHOX2B	synonymous	HNSC\|1\|512\|0.00195
-	chr4	41748308	41748308	C	T	exonic	PHOX2B	nonsynonymous	GBM\|1\|290\|0.00345,GBMLGG\|1\|820\|0.00122
-	chr4	41750496	41750496	A	T	exonic	PHOX2B	stopgain	SKCM\|1\|368\|0.00272
-	chr4	41748009	41748009	C	-	exonic	PHOX2B	frameshift	LIHC\|1\|373\|0.00268
-	chr4	41750513	41750513	C	T	exonic	PHOX2B	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr4	41749524	41749524	C	T	exonic	PHOX2B	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr4	41750608	41750608	G	T	exonic	PHOX2B	nonsynonymous	OV\|1\|469\|0.00213
-	chr4	41749508	41749508	C	T	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41748208	41748208	G	A	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
-	chr4	41749389	41749389	C	T	exonic	PHOX2B	nonsynonymous	BRCA\|1\|982\|0.00102,COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41749523	41749523	C	T	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41748160	41748160	G	A	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
-	chr4	41747973	41747973	C	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41748296	41748296	C	T	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41750611	41750611	T	C	exonic	PHOX2B	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr4	41750472	41750472	C	A	exonic	PHOX2B	synonymous	LUAD\|6\|543\|0.01105
-	chr4	41747938	41747938	G	-	exonic	PHOX2B	frameshift	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41748145	41748145	G	T	exonic	PHOX2B	stopgain	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41748171	41748171	G	A	exonic	PHOX2B	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr4	41750584	41750584	T	C	exonic	PHOX2B	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr4	41750491	41750491	G	T	exonic	PHOX2B	nonsynonymous	LUAD\|3\|543\|0.00552
-	chr4	41747879	41747879	G	A	exonic	PHOX2B	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr4	41749385	41749385	A	G	exonic	PHOX2B	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr4	41747940	41747940	G	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41748193	41748193	C	G	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
-	chr4	41749672	41749672	C	T	intronic	PHOX2B	unknown	UCEC\|1\|248\|0.00403
-	chr4	41749444	41749444	G	A	exonic	PHOX2B	synonymous	PAAD\|1\|185\|0.00541
-	chr4	41749478	41749478	G	C	exonic	PHOX2B	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr4	41748224	41748224	T	G	exonic	PHOX2B	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41750415	41750415	C	T	exonic	PHOX2B	synonymous	SKCM\|1\|368\|0.00272
-	chr4	41747870	41747870	C	G	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41748139	41748139	C	T	exonic	PHOX2B	synonymous	SKCM\|2\|368\|0.00543
-	chr4	41748111	41748111	G	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41748265	41748265	C	T	exonic	PHOX2B	synonymous	BRCA\|1\|982\|0.00102
-	chr4	41750422	41750422	G	T	exonic	PHOX2B	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
rs551983206	chr4	41749551	41749551	G	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41748140	41748140	G	A	exonic	PHOX2B	nonsynonymous	BLCA\|1\|396\|0.00253,PRAD\|1\|499\|0.00200
-	chr4	41748270	41748270	C	T	exonic	PHOX2B	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41747901	41747901	G	A	exonic	PHOX2B	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr4	41750502	41750502	G	T	exonic	PHOX2B	nonsynonymous	UCEC\|1\|248\|0.00403
rs543135182	chr4	41748004	41748004	C	T	exonic	PHOX2B	synonymous	LIHC\|1\|373\|0.00268
-	chr4	41749376	41749376	G	-	exonic	PHOX2B	frameshift	BLCA\|1\|396\|0.00253
-	chr4	41749393	41749393	C	G	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41750405	41750405	T	A	exonic	PHOX2B	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr4	41749373	41749373	C	T	exonic	PHOX2B	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr4	41749376	41749376	G	A	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs767837376	chr4	41748282	41748282	C	T	exonic	PHOX2B	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr4	41750604	41750604	-	A	exonic	PHOX2B	frameshift	BRCA\|1\|982\|0.00102
-	chr4	41750460	41750460	G	T	exonic	PHOX2B	synonymous	LUSC\|1\|178\|0.00562
-	chr4	41748152	41748152	G	T	exonic	PHOX2B	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr4	41748173	41748173	C	A	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
rs779068107	chr4	41747864	41747864	T	C	exonic	PHOX2B	nonsynonymous	THYM\|1\|123\|0.00813
-	chr4	41749496	41749496	C	T	exonic	PHOX2B	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr4	41747973	41747973	C	T	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41747863	41747863	G	A	exonic	PHOX2B	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr4	41747895	41747895	C	T	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41749416	41749416	T	G	exonic	PHOX2B	nonsynonymous	ACC\|1\|90\|0.01111
-	chr4	41750410	41750410	T	A	exonic	PHOX2B	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr4	41749396	41749396	C	T	exonic	PHOX2B	synonymous	BLCA\|1\|396\|0.00253

Disease information of PHOX2B

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
PHOX2B	Crohn Disease	C06	Disease or Syndrome	CTD_human
PHOX2B	Dysautonomia, Familial	C10;C16	Congenital Abnormality; Disease or Syndrome	GENOMICS_ENGLAND
PHOX2B	Neuroblastoma	C04	Neoplastic Process	CGI;CTD_human;ORPHANET
PHOX2B	Schizophrenia	F03	Mental or Behavioral Dysfunction	PSYGENET
PHOX2B	Crohn's disease of large bowel	C06	Disease or Syndrome	CTD_human
PHOX2B	Crohn's disease of the ileum	C06	Disease or Syndrome	CTD_human
PHOX2B	Regional enteritis	C06	Disease or Syndrome	CTD_human
PHOX2B	IIeocolitis	C06	Disease or Syndrome	CTD_human
PHOX2B	Congenital central hypoventilation	C08;C10;C23	Disease or Syndrome	CTD_human;ORPHANET;UNIPROT
PHOX2B	CCHS WITH HIRSCHSPRUNG DISEASE	C08;C10;C23	Congenital Abnormality; Disease or Syndrome	CTD_human;ORPHANET;UNIPROT
PHOX2B	Hirschsprung disease ganglioneuroblastoma	C04;C06;C16	Disease or Syndrome	ORPHANET
PHOX2B	Neural crest tumor	C04;C19	Disease or Syndrome	ORPHANET
PHOX2B	Intellectual Disability	C10;C23;F01;F03	Mental or Behavioral Dysfunction	GENOMICS_ENGLAND

Pathway associated with PHOX2B

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number
pathway0002747	Hs_Neural_Crest_Differentiation_WP2064_79263	wikipathways	40	129

Go term information of PHOX2B

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GO_term_name	GO_term_type	TF_name
GO_REGULATION_OF_RESPIRATORY_SYSTEM_PROCESS	BP	PHOX2B
GO_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE	BP	PHOX2B
GO_REGULATION_OF_RESPIRATORY_GASEOUS_EXCHANGE_BY_NEUROLOGICAL_SYSTEM_PROCESS	BP	PHOX2B
GO_CRANIAL_NERVE_DEVELOPMENT	BP	PHOX2B
GO_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_AMEBOIDAL_TYPE_CELL_MIGRATION	BP	PHOX2B
GO_POSITIVE_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION	BP	PHOX2B
GO_NEURAL_CREST_CELL_MIGRATION	BP	PHOX2B
GO_MESENCHYMAL_CELL_DIFFERENTIATION	BP	PHOX2B
GO_NEURAL_NUCLEUS_DEVELOPMENT	BP	PHOX2B
GO_CELLULAR_RESPONSE_TO_ORGANIC_SUBSTANCE	BP	PHOX2B
GO_NEGATIVE_REGULATION_OF_CELL_CYCLE_ARREST	BP	PHOX2B
GO_CELL_DIFFERENTIATION_IN_HINDBRAIN	BP	PHOX2B
GO_SYMPATHETIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_NERVE_DEVELOPMENT	BP	PHOX2B
GO_NEURON_PROJECTION_MORPHOGENESIS	BP	PHOX2B
GO_HEAD_DEVELOPMENT	BP	PHOX2B
GO_ENTERIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_CELL_MIGRATION_IN_HINDBRAIN	BP	PHOX2B
GO_AUTONOMIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_DOPAMINERGIC_NEURON_DIFFERENTIATION	BP	PHOX2B
GO_SKELETAL_MUSCLE_CELL_DIFFERENTIATION	BP	PHOX2B
GO_GANGLION_DEVELOPMENT	BP	PHOX2B
GO_CENTRAL_NERVOUS_SYSTEM_NEURON_DEVELOPMENT	BP	PHOX2B
GO_PARASYMPATHETIC_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_REGULATION_OF_CELL_DEVELOPMENT	BP	PHOX2B
GO_CENTRAL_NERVOUS_SYSTEM_DEVELOPMENT	BP	PHOX2B
GO_REGULATION_OF_RESPIRATORY_GASEOUS_EXCHANGE	BP	PHOX2B
GO_NEURAL_CREST_CELL_DIFFERENTIATION	BP	PHOX2B
GO_CENTRAL_NERVOUS_SYSTEM_NEURON_AXONOGENESIS	BP	PHOX2B
GO_NUCLEAR_CHROMATIN	CC	PHOX2B

Survival analysis of PHOX2B

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 PHOX2B

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