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 HEXB

Basic gene info.	Gene symbol	HEXB
	Gene name	hexosaminidase B (beta polypeptide)
	Synonyms	ENC-1AS\|HEL-248
	Cytomap	UCSC genome browser: 5q13
	Genomic location	chr5 :73980968-74017113
	Type of gene	protein-coding
	RefGenes	NM_000521.3, NM_001292004.1,
	Ensembl id	ENSG00000049860
	Description	HCC-7N-acetyl-beta-glucosaminidase subunit betabeta-N-acetylhexosaminidase subunit betabeta-hexosaminidase subunit betacervical cancer proto-oncogene 7 proteinepididymis luminal protein 248hexosaminidase subunit B
	Modification date	20141207
dbXrefs	MIM : 606873
	HGNC : HGNC
	Ensembl : ENSG00000049860
	HPRD : 06043
	Vega : OTTHUMG00000102057
Protein	UniProt: P07686 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HEXB
	BioGPS: 3074
	Gene Expression Atlas: ENSG00000049860
	The Human Protein Atlas: ENSG00000049860
Pathway	NCI Pathway Interaction Database: HEXB
	KEGG: HEXB
	REACTOME: HEXB
	ConsensusPathDB
	Pathway Commons: HEXB
Metabolism	MetaCyc: HEXB
	HUMANCyc: HEXB
Regulation	Ensembl's Regulation: ENSG00000049860
	miRBase: chr5 :73,980,968-74,017,113
	TargetScan: NM_000521
	cisRED: ENSG00000049860
Context	iHOP: HEXB
	cancer metabolism search in PubMed: HEXB
	UCL Cancer Institute: HEXB
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: HEXB
	Familial Cancer Database: HEXB

* 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
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_HYALURONAN_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	268800; phenotype. 606873; gene.
Orphanet	309155; Sandhoff disease, infantile form. 309162; Sandhoff disease, juvenile form. 309169; Sandhoff disease, adult form.
Disease	KEGG Disease: HEXB
	MedGen: HEXB (Human Medical Genetics with Condition)
	ClinVar: HEXB
Phenotype	MGI: HEXB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: HEXB

Mutations for HEXB

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HEXB related fusion information.

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

AA253363

HEXB

122

74017013

74017113

SSRP1

113

329

57095812

57097846

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

There's no copy number variation information in COSMIC data for this gene.

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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr5:73985215-73985215	p.K121R	4
chr5:73981270-73981270	p.L62S	2
chr5:74016557-74016557	p.R533H	2
chr5:74016341-74016341	p.L502F	2
chr5:74014197-74014197	p.?	2
chr5:74014631-74014631	p.G418R	1
chr5:73992858-73992858	p.R199K	1
chr5:74009438-74009438	p.G293G	1
chr5:73981280-73981280	p.M65I	1
chr5:74014632-74014632	p.G418A	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=1

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	2	3	1	5					1			1		1		1	3	4		8
# mutation	2	3	1	5					1			1		1		1	3	4		8
nonsynonymous SNV	2	3		4										1		1	3	3		5
synonymous SNV			1	1					1			1						1		3

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
chr5:73981270	p.M65I	1
chr5:74009342	p.E384D,HEXB	1
chr5:74014695	p.L72F	1
chr5:73981280	p.G401E,HEXB	1
chr5:74009374	p.Y78D	1
chr5:74014703	p.E407Q,HEXB	1
chr5:73981299	p.H102Y	1
chr5:74009401	p.A416A,HEXB	1
chr5:74016271	p.P141L	1
chr5:73981317	p.G418R,HEXB	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 HEXB 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 HEXB

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


ADAP2,AP3B1,C3AR1,CCPG1,CD68,CTSB,CTSL, FCER1G,GM2A,HAVCR2,HEXB,LILRA2,LIPA,MFSD1, MSR1,PSAP,SIGLEC9,SNX2,TPP1,TXNDC15,YIPF5	AIF1,ANXA4,ARPC5,C1orf162,CCDC109B,CD86,CPVL, FCER1G,GPNMB,HEXB,HPGDS,LY96,MFSD1,MS4A6A, NPC2,OSTF1,PRCP,SH3BGRL3,SLC38A6,SLC7A7,TMSB4XP8

ANKRA2,TRAPPC13,CETN3,COX7C,GFM2,HEXB,LYRM7, LYSMD3,MRPS36,NDFIP1,NDUFB5,PAPD4,RNF14,SAR1B, SLC25A46,SLC30A5,SNX2,TAF9,TMEM161B,TMEM167A,ZCCHC10	C11orf54,CASP6,EIF2AK1,FUCA2,GPBP1L1,HEXB,MFSD1, PAFAH2,PLBD1,SH3BGRL2,SLC35B3,SLC35D2,SPTLC1,TMEM144, TMEM59,TMEM9B,VAV3,XK,ZDHHC3,ZNF823,ZNRF2

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 HEXB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P07686; -.
Chemistry	ChEMBL	CHEMBL3038485; -.
Organism-specific databases	PharmGKB	PA29257; -.
Organism-specific databases	CTD	3074; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB02813	hexosaminidase B (beta polypeptide)	experimental	2-Acetamido-2-Deoxy-D-Glucono-1,5-Lactone
DB03747	hexosaminidase B (beta polypeptide)	experimental	3ar,5r,6s,7r,7ar-5-Hydroxymethyl-2-Methyl-5,6,7,7a-Tetrahydro-3ah-Pyrano[3,2-D]Thiazole-6,7-Diol
DB03861	hexosaminidase B (beta polypeptide)	experimental	(2r,3r,4s,5r)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium

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Cross referenced IDs for HEXB

* 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