Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 CD44

Basic gene info.	Gene symbol	CD44
	Gene name	CD44 molecule (Indian blood group)
	Synonyms	CDW44\|CSPG8\|ECMR-III\|HCELL\|HUTCH-I\|IN\|LHR\|MC56\|MDU2\|MDU3\|MIC4\|Pgp1
	Cytomap	UCSC genome browser: 11p13
	Genomic location	chr11 :35160416-35253949
	Type of gene	protein-coding
	RefGenes	NM_000610.3, NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1, NM_001202555.1,NM_001202556.1,NM_001202557.1,
	Ensembl id	ENSG00000026508
	Description	CD44 antigenGP90 lymphocyte homing/adhesion receptorHermes antigencell surface glycoprotein CD44chondroitin sulfate proteoglycan 8epicanextracellular matrix receptor IIIhematopoietic cell E- and L-selectin ligandheparan sulfate proteoglycanhoming
	Modification date	20141222
dbXrefs	MIM : 107269
	HGNC : HGNC
	Ensembl : ENSG00000026508
	HPRD : 00115
	Vega : OTTHUMG00000044388
Protein	UniProt: P16070 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CD44
	BioGPS: 960
	Gene Expression Atlas: ENSG00000026508
	The Human Protein Atlas: ENSG00000026508
Pathway	NCI Pathway Interaction Database: CD44
	KEGG: CD44
	REACTOME: CD44
	ConsensusPathDB
	Pathway Commons: CD44
Metabolism	MetaCyc: CD44
	HUMANCyc: CD44
Regulation	Ensembl's Regulation: ENSG00000026508
	miRBase: chr11 :35,160,416-35,253,949
	TargetScan: NM_000610
	cisRED: ENSG00000026508
Context	iHOP: CD44
	cancer metabolism search in PubMed: CD44
	UCL Cancer Institute: CD44
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CD44 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_HYALURONAN_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	107269; gene. 107269; gene. 172290; gene. 172290; gene. 609027; phenotype. 609027; phenotype.
Orphanet
Disease	KEGG Disease: CD44
	MedGen: CD44 (Human Medical Genetics with Condition)
	ClinVar: CD44
Phenotype	MGI: CD44 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	CD44	chr11	35186096	35186116		chr11	36267498	36267518

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CD44 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
DA471107	CD44	1	204	11	35160718	35160921	PDHX	200	567	11	34952950	34979115
BP270776	NAA10	1	325	X	153197866	153200438	CD44	320	583	11	35251215	35251476
BE695450	SON	22	230	21	34929527	34929965	CD44	217	320	11	35250784	35250887
BI038422	CD44	5	151	11	35194829	35194974	COX15	151	392	10	101486747	101487274
AW376462	CD44	1	57	11	35252818	35252874	CD44	52	487	11	35252927	35253360
BF748398	CD44	1	177	11	35201902	35211434	SLC4A2	168	376	7	150772771	150773216
AW580058	CD44	1	148	11	35222883	35223031	CD44	144	374	11	35223063	35223293
BM280254	CD44	18	147	11	35250886	35251015	CD44	143	303	11	35250675	35250835
AW935153	TMEM50B	12	369	21	34821524	34821880	CD44	370	617	11	35233263	35233511
EY123442	CD44	8	295	11	35250716	35251011	SERINC5	289	310	5	79453346	79453367

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	1					2		1		1				3
GAIN (# sample)	1						1		1		1				3
LOSS (# sample)	1	1					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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr11:35236420-35236420	p.P611H	3
chr11:35198160-35198160	p.V36M	2
chr11:35198181-35198181	p.S43G	2
chr11:35219741-35219741	p.L290L	2
chr11:35232825-35232825	p.P547A	2
chr11:35227753-35227753	p.H459Q	2
chr11:35232846-35232846	p.T554A	2
chr11:35226171-35226171	p.S422S	2
chr11:35201842-35201842	p.H85H	2
chr11:35231516-35231516	p.Q507H	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1	1	6	1		2		2			5	4	1			3	8	2	7
# mutation		1	1	6	1		2		2			6	4	1			3	8	2	10
nonsynonymous SNV			1	5	1		1		2			3	4	1			3	5	1	4
synonymous SNV		1		1			1					3						3	1	6

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr11:35198160	p.S379S,CD44	2
chr11:35226171	p.V36M,CD44	2
chr11:35250752	p.S45S,CD44	1
chr11:35211510	p.G251E,CD44	1
chr11:35223242	p.M418V,CD44	1
chr11:35227679	p.R46W,CD44	1
chr11:35250813	p.D257Y,CD44	1
chr11:35211585	p.Q258H,CD44	1
chr11:35223298	p.T47M,CD44	1
chr11:35198189	p.R270L,CD44	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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