Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for CDX2
Basic gene info.Gene symbolCDX2
Gene namecaudal type homeobox 2
SynonymsCDX-3|CDX2/AS|CDX3
CytomapUCSC genome browser: 13q12.3
Genomic locationchr13 :28536204-28543505
Type of geneprotein-coding
RefGenesNM_001265.4,
Ensembl idENSG00000165556
Descriptioncaudal type homeo box transcription factor 2caudal type homeobox transcription factor 2caudal-type homeobox protein 2homeobox protein CDX-2
Modification date20141222
dbXrefs MIM : 600297
HGNC : HGNC
HPRD : 02622
ProteinUniProt: Q99626
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CDX2
BioGPS: 1045
Gene Expression Atlas: ENSG00000165556
The Human Protein Atlas: ENSG00000165556
PathwayNCI Pathway Interaction Database: CDX2
KEGG: CDX2
REACTOME: CDX2
ConsensusPathDB
Pathway Commons: CDX2
MetabolismMetaCyc: CDX2
HUMANCyc: CDX2
RegulationEnsembl's Regulation: ENSG00000165556
miRBase: chr13 :28,536,204-28,543,505
TargetScan: NM_001265
cisRED: ENSG00000165556
ContextiHOP: CDX2
cancer metabolism search in PubMed: CDX2
UCL Cancer Institute: CDX2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CDX2 in cancer cell metabolism1. Herr R, Kohler M, Andrlova H, Weinberg F, Moller Y, et al. (2015) B-Raf inhibitors induce epithelial differentiation in BRAF-mutant colorectal cancer cells. Cancer Res 75: 216-229. doi: 10.1158/0008-5472.CAN-13-3686. go to article
2. Coskun M, Olsen AK, Bzorek M, Holck S, Engel UH, et al. (2014) Involvement of CDX2 in the cross talk between TNF-alpha and Wnt signaling pathway in the colon cancer cell line Caco-2. Carcinogenesis 35: 1185-1192. doi: 10.1093/carcin/bgu037. go to article
3. Modica S, Cariello M, Morgano A, Gross I, Vegliante MC, et al. (2014) Transcriptional regulation of the intestinal nuclear bile acid farnesoid X receptor (FXR) by the caudal-related homeobox 2 (CDX2). J Biol Chem 289: 28421-28432. doi: 10.1074/jbc.M114.571513. pmid: 4192494. go to article

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Phenotypic Information for CDX2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CDX2
Familial Cancer Database: CDX2
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 600297; gene.
Orphanet
DiseaseKEGG Disease: CDX2
MedGen: CDX2 (Human Medical Genetics with Condition)
ClinVar: CDX2
PhenotypeMGI: CDX2 (International Mouse Phenotyping Consortium)
PhenomicDB: CDX2

Mutations for CDX2
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CDX2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr13:28537278-28537278p.V306fs*24
chr13:28542958-28542958p.G62G2
chr13:28537485-28537485p.R237C2
chr13:28543033-28543033p.Y37Y2
chr13:28537332-28537332p.L288V1
chr13:28543092-28543092p.V18L1
chr13:28539053-28539053p.R214Q1
chr13:28542688-28542688p.A152A1
chr13:28537373-28537373p.P274H1
chr13:28539058-28539058p.T212T1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 21      43   51 5
# mutation 1 21      43   51 7
nonsynonymous SNV   21      13   21 6
synonymous SNV 1         3    3  1
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr13:28537485p.R237C2
chr13:28537390p.P260P1
chr13:28539094p.F31F1
chr13:28537404p.Q253E1
chr13:28539140p.E241K1
chr13:28537414p.A239V1
chr13:28542661p.A221T1
chr13:28537437p.R214Q1
chr13:28542705p.T212T1
chr13:28537473p.R209H1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for CDX2 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for CDX2

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ALDH3A1,BCL2L10,C4orf17,CDX2,GAGE12J,GAGE13,GAGE2B,
GAGE8,GPX2,GRIN2D,HOXD11,HOXD13,IQCF2,LOC285629,
NKX2-4,RBMXL2,UGT1A5,VCX,VCX3A,VCX3B,VCY
ANXA10,BAAT,CDX2,CTSE,GKN2,IGF2BP1,KRTAP13-1,
MAGEA4,NAPSA,NKX2-1,PAEP,BPIFA1,PSAPL1,SCGB3A2,
SFTA3,SFTPB,SLC26A9,SPINK1,TM4SF20,TM4SF5,UGT1A10

AIFM3,NOL4L,CDX2,GPR160,IHH,MAP1LC3A,OVOL1,
PIGU,PLAGL2,POFUT1,PPP1R14C,PRDX5,PRR15,PXMP4,
RALY,RNF114,RNF43,SATB2,STK38,TM9SF4,VAV3
ACSS2,CAPN5,CDX2,FRAT2,GPRC5C,HES1,HNF1B,
IKBKE,LDLRAP1,LGALS9,NR2F6,PGM1,PIGR,PPFIA3,
PPP1R14D,RALY,SDC1,SLC44A4,TMEM102,TPRN,TRAF3IP2
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for CDX2


There's no related Drug.
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Cross referenced IDs for CDX2
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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