Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 CD44
Basic gene info.Gene symbolCD44
Gene nameCD44 molecule (Indian blood group)
SynonymsCDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1
CytomapUCSC genome browser: 11p13
Genomic locationchr11 :35160416-35253949
Type of geneprotein-coding
RefGenesNM_000610.3,
NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,
NM_001202555.1,NM_001202556.1,NM_001202557.1,
Ensembl idENSG00000026508
DescriptionCD44 antigenGP90 lymphocyte homing/adhesion receptorHermes antigencell surface glycoprotein CD44chondroitin sulfate proteoglycan 8epicanextracellular matrix receptor IIIhematopoietic cell E- and L-selectin ligandheparan sulfate proteoglycanhoming
Modification date20141222
dbXrefs MIM : 107269
HGNC : HGNC
Ensembl : ENSG00000026508
HPRD : 00115
Vega : OTTHUMG00000044388
ProteinUniProt: P16070
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CD44
BioGPS: 960
Gene Expression Atlas: ENSG00000026508
The Human Protein Atlas: ENSG00000026508
PathwayNCI Pathway Interaction Database: CD44
KEGG: CD44
REACTOME: CD44
ConsensusPathDB
Pathway Commons: CD44
MetabolismMetaCyc: CD44
HUMANCyc: CD44
RegulationEnsembl's Regulation: ENSG00000026508
miRBase: chr11 :35,160,416-35,253,949
TargetScan: NM_000610
cisRED: ENSG00000026508
ContextiHOP: CD44
cancer metabolism search in PubMed: CD44
UCL Cancer Institute: CD44
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CD44 in cancer cell metabolism1. Misra S, Hascall VC, Markwald RR, Ghatak S (2015) Interactions between Hyaluronan and Its Receptors (CD44, RHAMM) Regulate the Activities of Inflammation and Cancer. Front Immunol 6: 201. doi: 10.3389/fimmu.2015.00201. pmid: 4422082 go to article
2. Takahashi H, Nishimura J, Kagawa Y, Kano Y, Takahashi Y, et al. (2015) Significance of Polypyrimidine Tract-Binding Protein 1 Expression in Colorectal Cancer. Mol Cancer Ther 14: 1705-1716. doi: 10.1158/1535-7163.MCT-14-0142. go to article

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Phenotypic Information for CD44(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CD44
Familial Cancer Database: CD44
* 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_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 107269; gene.
107269; gene.
172290; gene.
172290; gene.
609027; phenotype.
609027; phenotype.
Orphanet
DiseaseKEGG Disease: CD44
MedGen: CD44 (Human Medical Genetics with Condition)
ClinVar: CD44
PhenotypeMGI: CD44 (International Mouse Phenotyping Consortium)
PhenomicDB: CD44

Mutations for CD44
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasCD44chr113518609635186116chr113626749836267518
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CD44 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample21    2 1 1   3  
GAIN (# sample)1     1 1 1   3  
LOSS (# sample)11    1          
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=2)
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
chr11:35236420-35236420p.P611H3
chr11:35198160-35198160p.V36M2
chr11:35198181-35198181p.S43G2
chr11:35219741-35219741p.L290L2
chr11:35232825-35232825p.P547A2
chr11:35227753-35227753p.H459Q2
chr11:35232846-35232846p.T554A2
chr11:35226171-35226171p.S422S2
chr11:35201842-35201842p.H85H2
chr11:35231516-35231516p.Q507H1

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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 1161 2 2  541  3827
# mutation 1161 2 2  641  38210
nonsynonymous SNV  151 1 2  341  3514
synonymous SNV 1 1  1    3     316
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
chr11:35198160p.S379S,CD442
chr11:35226171p.V36M,CD442
chr11:35250752p.S45S,CD441
chr11:35211510p.G251E,CD441
chr11:35223242p.M418V,CD441
chr11:35227679p.R46W,CD441
chr11:35250813p.D257Y,CD441
chr11:35211585p.Q258H,CD441
chr11:35223298p.T47M,CD441
chr11:35198189p.R270L,CD441

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 CD44 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 CD44

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

ARHGEF6,C1QL3,BPIFB3,CAPRIN1,CAT,CD44,CD59,
CYP7A1,DMBT1,EMR3,GPR85,MROH2B,HIPK3,MUC7,
PDHX,BPIFA1,SLC1A2,SLC6A14,TRAF6,TRIM44,VMO1
ANKRD13A,APOBEC3C,ARF6,TMEM248,CD44,CMTM6,DAZAP2,
DRAM1,FAM102B,FRMD4B,GLT8D1,LHFPL2,LOC151162,MPZL1,
MYOF,PTGFRN,PTPN9,RERG,SLC16A4,SLC37A3,SNX7

AHR,ATP1B1,BACE2,CAPRIN1,CD44,CLDN2,YBX3,
EEF2,MANBA,PKNOX1,PLA2G4A,PPP3CA,RASAL1,RNF144B,
RNF145,SRD5A3,TC2N,TLE1,TMEM173,TNFRSF11A,ZBTB8A
ACSL4,CD44,DOC2B,HGF,IFI16,IKBIP,LMAN1,
LPCAT1,LRP8,MSTO1,NEIL2,PDPN,PTGFR,RAMP3,
RIPK2,SELP,SLC43A3,SLFN11,SRM,ST3GAL5,XPOT
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 CD44


There's no related Drug.
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Cross referenced IDs for CD44
* 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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