Cancer CRCdb

TF information

TF name:	MSX2
TF family:	Homeobox
Ensembl gene ID:	ENSG00000120149
Ensembl protein ID:	ENSP00000239243
Entrez gene ID:	4488

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

Frequency of MSX2 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_01_068	Cell line	Prostate: derived from metastatic site: vertebral metastasis	VCaP	0.12328767123288
Sample_02_021	Cell line	Colon	V429	0.37849524358605
Sample_02_079	Cell line	Mammary Gland	T-47D_1	0.44444444444444
Sample_02_197	Cell line	Stomach	SNU1750	0.22222222222222
Sample_02_242	Cell line	Colon	V481	0.40902390565917
Sample_02_322	Cell line	Colon	Caco-2	0.16689098250336
Sample_02_354	Cell line	Colon	Colo205	0.21021021021021

MSX2 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name
Sample_02_242	Colon	Cell line	V481

MSX2 distribution in all CRCs

Genomic distribution of SEs associated with MSX2

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Mutation of MSX2

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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 MSX2

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
-	chr5	174156417	174156417	C	T	exonic	MSX2	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr5	174156441	174156441	T	C	exonic	MSX2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr5	174156278	174156278	T	C	exonic	MSX2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr5	174156457	174156457	C	A	exonic	MSX2	synonymous	SARC\|1\|247\|0.00405
rs150352201	chr5	174156373	174156373	G	A	exonic	MSX2	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr5	174156278	174156278	T	A	exonic	MSX2	nonsynonymous	OV\|1\|469\|0.00213
rs754536048	chr5	174156216	174156216	C	T	exonic	MSX2	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr5	174156337	174156337	G	T	exonic	MSX2	nonsynonymous	HNSC\|2\|512\|0.00391
-	chr5	174156269	174156269	C	T	exonic	MSX2	stopgain	BRCA\|1\|982\|0.00102
-	chr5	174156219	174156219	G	A	exonic	MSX2	nonsynonymous	COAD\|3\|367\|0.00817,COADREAD\|3\|489\|0.00613
-	chr5	174156247	174156247	C	T	exonic	MSX2	synonymous	SKCM\|2\|368\|0.00543
-	chr5	174156454	174156454	C	T	exonic	MSX2	synonymous	PRAD\|1\|499\|0.00200
-	chr5	174151740	174151740	G	C	exonic	MSX2	synonymous	UCS\|1\|57\|0.01754
-	chr5	174156192	174156192	G	T	exonic	MSX2	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr5	174156222	174156222	C	T	exonic	MSX2	nonsynonymous	PRAD\|1\|499\|0.00200
-	chr5	174151962	174151962	G	A	exonic	MSX2	synonymous	LIHC\|1\|373\|0.00268
-	chr5	174156283	174156283	C	T	exonic	MSX2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr5	174156377	174156377	A	T	exonic	MSX2	stopgain	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr5	174156555	174156555	C	T	exonic	MSX2	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr5	174156265	174156265	C	T	exonic	MSX2	synonymous	SKCM\|1\|368\|0.00272
rs756013230	chr5	174156285	174156285	C	T	exonic	MSX2	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr5	174156254	174156254	G	A	exonic	MSX2	nonsynonymous	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
-	chr5	174152037	174152037	G	A	exonic	MSX2	synonymous	ACC\|1\|90\|0.01111
-	chr5	174156513	174156513	G	T	exonic	MSX2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr5	174156363	174156363	G	C	exonic	MSX2	nonsynonymous	TGCT\|1\|155\|0.00645
rs186769394	chr5	174156169	174156169	G	A	exonic	MSX2	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr5	174156184	174156184	C	T	exonic	MSX2	synonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
-	chr5	174156477	174156477	C	T	exonic	MSX2	nonsynonymous	BRCA\|1\|982\|0.00102
rs367897914	chr5	174152000	174152000	C	T	exonic	MSX2	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr5	174152030	174152030	C	T	exonic	MSX2	nonsynonymous	GBM\|1\|290\|0.00345,GBMLGG\|1\|820\|0.00122
rs766427771	chr5	174151701	174151701	C	T	exonic	MSX2	synonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820

Disease information of MSX2

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
MSX2	Craniosynostosis	C05;C16	Disease or Syndrome	GENOMICS_ENGLAND
MSX2	Craniofacial Abnormalities	C05;C16	Congenital Abnormality	CTD_human
MSX2	Female Urogenital Diseases	C13	Disease or Syndrome	CTD_human
MSX2	CRANIOSYNOSTOSIS, TYPE 2	C05;C16	Disease or Syndrome	CTD_human;ORPHANET;UNIPROT
MSX2	Parietal Foramina With Cleidocranial Dysplasia	C05;C10;C16;C23	Disease or Syndrome	CTD_human;ORPHANET
MSX2	PARIETAL FORAMINA	C10;C16;C23	Congenital Abnormality	CTD_human;ORPHANET;UNIPROT
MSX2	PARIETAL FORAMINA 1	C10;C16;C23	Congenital Abnormality	UNIPROT
MSX2	Intellectual Disability	C10;C23;F01;F03	Mental or Behavioral Dysfunction	GENOMICS_ENGLAND

Pathway associated with MSX2

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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 MSX2

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GO_term_name	GO_term_type	TF_name
GO_NEGATIVE_REGULATION_OF_TRANSCRIPTION_REGULATORY_REGION_DNA_BINDING	BP	MSX2
GO_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS	BP	MSX2
GO_REGULATION_OF_FAT_CELL_DIFFERENTIATION	BP	MSX2
GO_MAMMARY_GLAND_MORPHOGENESIS	BP	MSX2
GO_BONE_TRABECULA_MORPHOGENESIS	BP	MSX2
GO_CARDIAC_SEPTUM_DEVELOPMENT	BP	MSX2
GO_GLAND_MORPHOGENESIS	BP	MSX2
GO_OUTFLOW_TRACT_SEPTUM_MORPHOGENESIS	BP	MSX2
GO_CARDIAC_CHAMBER_MORPHOGENESIS	BP	MSX2
GO_REGULATION_OF_EPIDERMIS_DEVELOPMENT	BP	MSX2
GO_NEGATIVE_REGULATION_OF_FAT_CELL_DIFFERENTIATION	BP	MSX2
GO_EMBRYONIC_DIGIT_MORPHOGENESIS	BP	MSX2
GO_HINDLIMB_MORPHOGENESIS	BP	MSX2
GO_ENDOCARDIAL_CUSHION_DEVELOPMENT	BP	MSX2
GO_REGULATION_OF_MEIOTIC_NUCLEAR_DIVISION	BP	MSX2
GO_MAMMARY_GLAND_EPITHELIUM_DEVELOPMENT	BP	MSX2
GO_MORPHOGENESIS_OF_AN_EPITHELIUM	BP	MSX2
GO_FORELIMB_MORPHOGENESIS	BP	MSX2
GO_CHONDROCYTE_DEVELOPMENT	BP	MSX2
GO_TOOTH_MINERALIZATION	BP	MSX2
GO_REGULATION_OF_HAIR_CYCLE	BP	MSX2
GO_REGULATION_OF_MEIOTIC_CELL_CYCLE	BP	MSX2
GO_BONE_GROWTH	BP	MSX2
GO_ENDOCARDIAL_CUSHION_MORPHOGENESIS	BP	MSX2
GO_EPITHELIAL_TO_MESENCHYMAL_TRANSITION	BP	MSX2
GO_REGULATION_OF_HAIR_FOLLICLE_DEVELOPMENT	BP	MSX2
GO_ENDOCARDIAL_CUSHION_FORMATION	BP	MSX2
GO_NEGATIVE_REGULATION_OF_DNA_BINDING	BP	MSX2
GO_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER	BP	MSX2
GO_POSITIVE_REGULATION_OF_MEIOTIC_CELL_CYCLE	BP	MSX2
GO_POSITIVE_REGULATION_OF_BMP_SIGNALING_PATHWAY	BP	MSX2
GO_ENAMEL_MINERALIZATION	BP	MSX2
GO_MESENCHYMAL_CELL_DIFFERENTIATION	BP	MSX2
GO_EMBRYONIC_FORELIMB_MORPHOGENESIS	BP	MSX2
GO_REGULATION_OF_MESENCHYMAL_CELL_APOPTOTIC_PROCESS	BP	MSX2
GO_POSITIVE_REGULATION_OF_CELL_DIVISION	BP	MSX2
GO_TRABECULA_MORPHOGENESIS	BP	MSX2
GO_MORPHOGENESIS_OF_AN_EPITHELIAL_SHEET	BP	MSX2
GO_APPENDAGE_DEVELOPMENT	BP	MSX2
GO_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS	BP	MSX2
GO_POSITIVE_REGULATION_OF_HAIR_CYCLE	BP	MSX2
GO_EMBRYONIC_HINDLIMB_MORPHOGENESIS	BP	MSX2
GO_ORGAN_GROWTH	BP	MSX2
GO_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND	BP	MSX2
GO_POSITIVE_REGULATION_OF_EPIDERMIS_DEVELOPMENT	BP	MSX2
GO_EPIBOLY	BP	MSX2
GO_CRANIAL_SKELETAL_SYSTEM_DEVELOPMENT	BP	MSX2
GO_NEGATIVE_REGULATION_OF_EPIDERMIS_DEVELOPMENT	BP	MSX2
GO_NEGATIVE_REGULATION_OF_BINDING	BP	MSX2
GO_AMELOGENESIS	BP	MSX2
GO_OSSIFICATION	BP	MSX2
GO_REGULATION_OF_EPIDERMAL_CELL_DIFFERENTIATION	BP	MSX2
GO_REGULATION_OF_OSTEOBLAST_DIFFERENTIATION	BP	MSX2
GO_NEGATIVE_REGULATION_OF_EPIDERMAL_CELL_DIFFERENTIATION	BP	MSX2
GO_MORPHOGENESIS_OF_A_BRANCHING_STRUCTURE	BP	MSX2
GO_NEGATIVE_REGULATION_OF_EPITHELIAL_CELL_DIFFERENTIATION	BP	MSX2
GO_CELLULAR_RESPONSE_TO_ALCOHOL	BP	MSX2
GO_REGULATION_OF_KERATINOCYTE_DIFFERENTIATION	BP	MSX2
GO_REGULATION_OF_BMP_SIGNALING_PATHWAY	BP	MSX2
GO_CELLULAR_RESPONSE_TO_ESTROGEN_STIMULUS	BP	MSX2
GO_ODONTOGENESIS_OF_DENTIN_CONTAINING_TOOTH	BP	MSX2
GO_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_INVOLVED_IN_ENDOCARDIAL_CUSHION_FORMATION	BP	MSX2
GO_POSITIVE_REGULATION_OF_OSTEOBLAST_DIFFERENTIATION	BP	MSX2
GO_OSTEOBLAST_DEVELOPMENT	BP	MSX2
GO_BONE_MORPHOGENESIS	BP	MSX2
GO_CARDIAC_EPITHELIAL_TO_MESENCHYMAL_TRANSITION	BP	MSX2
GO_CELLULAR_RESPONSE_TO_ESTRADIOL_STIMULUS	BP	MSX2
GO_TRABECULA_FORMATION	BP	MSX2
GO_OUTFLOW_TRACT_MORPHOGENESIS	BP	MSX2
GO_POSITIVE_REGULATION_OF_NUCLEAR_DIVISION	BP	MSX2
GO_WOUND_HEALING_SPREADING_OF_EPIDERMAL_CELLS	BP	MSX2
GO_CRANIOFACIAL_SUTURE_MORPHOGENESIS	BP	MSX2
GO_CARDIAC_SEPTUM_MORPHOGENESIS	BP	MSX2
GO_CELL_SURFACE_RECEPTOR_SIGNALING_PATHWAY_INVOLVED_IN_HEART_DEVELOPMENT	BP	MSX2
GO_MESENCHYME_MORPHOGENESIS	BP	MSX2
GO_MAMMARY_GLAND_DUCT_MORPHOGENESIS	BP	MSX2
GO_REGULATION_OF_TRANSCRIPTION_REGULATORY_REGION_DNA_BINDING	BP	MSX2
GO_NEGATIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER	BP	MSX2
GO_BRANCHING_INVOLVED_IN_MAMMARY_GLAND_DUCT_MORPHOGENESIS	BP	MSX2
GO_REGIONALIZATION	BP	MSX2
GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY	BP	MSX2
GO_REGULATION_OF_OSSIFICATION	BP	MSX2
GO_SIGNAL_TRANSDUCTION_INVOLVED_IN_REGULATION_OF_GENE_EXPRESSION	BP	MSX2
GO_TRANSCRIPTIONAL_REPRESSOR_ACTIVITY_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_BINDING	MF	MSX2
GO_SEQUENCE_SPECIFIC_DNA_BINDING	MF	MSX2

Survival analysis of MSX2

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 MSX2

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