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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CDX2 |
Basic gene info. | Gene symbol | CDX2 |
Gene name | caudal type homeobox 2 | |
Synonyms | CDX-3|CDX2/AS|CDX3 | |
Cytomap | UCSC genome browser: 13q12.3 | |
Genomic location | chr13 :28536204-28543505 | |
Type of gene | protein-coding | |
RefGenes | NM_001265.4, | |
Ensembl id | ENSG00000165556 | |
Description | caudal type homeo box transcription factor 2caudal type homeobox transcription factor 2caudal-type homeobox protein 2homeobox protein CDX-2 | |
Modification date | 20141222 | |
dbXrefs | MIM : 600297 | |
HGNC : HGNC | ||
HPRD : 02622 | ||
Protein | UniProt: Q99626 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CDX2 | |
BioGPS: 1045 | ||
Gene Expression Atlas: ENSG00000165556 | ||
The Human Protein Atlas: ENSG00000165556 | ||
Pathway | NCI Pathway Interaction Database: CDX2 | |
KEGG: CDX2 | ||
REACTOME: CDX2 | ||
ConsensusPathDB | ||
Pathway Commons: CDX2 | ||
Metabolism | MetaCyc: CDX2 | |
HUMANCyc: CDX2 | ||
Regulation | Ensembl's Regulation: ENSG00000165556 | |
miRBase: chr13 :28,536,204-28,543,505 | ||
TargetScan: NM_001265 | ||
cisRED: ENSG00000165556 | ||
Context | iHOP: CDX2 | |
cancer metabolism search in PubMed: CDX2 | ||
UCL Cancer Institute: CDX2 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of CDX2 in cancer cell metabolism | 1. 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) |
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Cancer | CGAP: CDX2 |
Familial Cancer Database: CDX2 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
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REACTOME_INTEGRATION_OF_ENERGY_METABOLISM |
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OMIM | 600297; gene. |
Orphanet | |
Disease | KEGG Disease: CDX2 |
MedGen: CDX2 (Human Medical Genetics with Condition) | |
ClinVar: CDX2 | |
Phenotype | MGI: 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CDX2 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=21) | (# total SNVs=9) |
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(# total SNVs=4) | (# total SNVs=0) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr13:28537278-28537278 | p.V306fs*2 | 4 |
chr13:28542958-28542958 | p.G62G | 2 |
chr13:28537485-28537485 | p.R237C | 2 |
chr13:28543033-28543033 | p.Y37Y | 2 |
chr13:28539033-28539033 | p.A221T | 1 |
chr13:28542666-28542666 | p.G160C | 1 |
chr13:28537332-28537332 | p.L288V | 1 |
chr13:28543092-28543092 | p.V18L | 1 |
chr13:28539053-28539053 | p.R214Q | 1 |
chr13:28542688-28542688 | p.A152A | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 2 | 1 |   |   |   |   |   |   | 4 | 3 |   |   |   | 5 | 1 |   | 5 |
# mutation |   | 1 |   | 2 | 1 |   |   |   |   |   |   | 4 | 3 |   |   |   | 5 | 1 |   | 7 |
nonsynonymous SNV |   |   |   | 2 | 1 |   |   |   |   |   |   | 1 | 3 |   |   |   | 2 | 1 |   | 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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr13:28537485 | p.R237C | 2 |
chr13:28539068 | p.P260P | 1 |
chr13:28537390 | p.F31F | 1 |
chr13:28539094 | p.Q253E | 1 |
chr13:28537404 | p.E241K | 1 |
chr13:28539140 | p.A239V | 1 |
chr13:28537414 | p.A221T | 1 |
chr13:28542661 | p.R214Q | 1 |
chr13:28537437 | p.T212T | 1 |
chr13:28542705 | p.R209H | 1 |
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* 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. |
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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 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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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 |
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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 |
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* 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 |
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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 |
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