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 GANAB

Basic gene info.	Gene symbol	GANAB
	Gene name	glucosidase, alpha; neutral AB
	Synonyms	G2AN\|GLUII
	Cytomap	UCSC genome browser: 11q12.3
	Genomic location	chr11 :62392299-62414104
	Type of gene	protein-coding
	RefGenes	NM_014610.3, NM_001278192.1,NM_001278193.1,NM_001278194.1,NM_198334.2, NM_198335.3,
	Ensembl id	ENSG00000089597
	Description	HEL-S-164nAalpha glucosidase II alpha subunitalpha-glucosidase 2epididymis secretory sperm binding protein Li 164nAglucosidase II subunit alphaneutral alpha-glucosidase AB
	Modification date	20141207
dbXrefs	MIM : 104160
	HGNC : HGNC
	Ensembl : ENSG00000089597
	HPRD : 03516
	Vega : OTTHUMG00000167696
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GANAB
	BioGPS: 23193
	Gene Expression Atlas: ENSG00000089597
	The Human Protein Atlas: ENSG00000089597
Pathway	NCI Pathway Interaction Database: GANAB
	KEGG: GANAB
	REACTOME: GANAB
	ConsensusPathDB
	Pathway Commons: GANAB
Metabolism	MetaCyc: GANAB
	HUMANCyc: GANAB
Regulation	Ensembl's Regulation: ENSG00000089597
	miRBase: chr11 :62,392,299-62,414,104
	TargetScan: NM_014610
	cisRED: ENSG00000089597
Context	iHOP: GANAB
	cancer metabolism search in PubMed: GANAB
	UCL Cancer Institute: GANAB
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: GANAB
	Familial Cancer Database: GANAB

* 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_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: GANAB
	MedGen: GANAB (Human Medical Genetics with Condition)
	ClinVar: GANAB
Phenotype	MGI: GANAB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GANAB

Mutations for GANAB

* 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 GANAB 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
DA340619	RAMP1	1	247	2	238768266	238786006	GANAB	244	583	11	62406459	62407205
AK295899	RAMP1	1	246	2	238768266	238786006	GANAB	243	3424	11	62392904	62407205
DB067719	TRAF6	1	230	11	36531596	36531822	GANAB	228	465	11	62406560	62407204
AI339818	ASNA1	10	192	19	12858955	12859137	GANAB	193	284	11	62392488	62392579
DW439793	RPL18	18	114	19	49119986	49120082	GANAB	114	189	11	62392305	62392381
BF085691	GANAB	12	74	11	62408925	62408987	STX7	68	175	6	132824675	132834200
BF514651	RPS6	17	330	9	19376253	19378387	GANAB	329	405	11	62406928	62407163
BF987702	GANAB	1	190	11	62393060	62393248	GANAB	178	432	11	62394517	62396350
BE710656	GANAB	14	111	11	62392762	62392861	GANAB	107	296	11	62392952	62393141
AA557976	GANAB	7	114	11	62392736	62392843	GANAB	112	357	11	62392841	62393086
BF893584	GRM8	171	204	7	126524936	126524998	GANAB	204	463	11	62392486	62393205
BE773523	PRKCSH	1	62	19	11557098	11557160	GANAB	55	159	11	62407307	62407411

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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=79)	Stat. for Synonymous SNVs (# total SNVs=19)

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
chr11:62396762-62396762	p.V614M	3
chr11:62400658-62400658	p.Y239C	2
chr11:62407101-62407101	p.C47C	2
chr11:62400050-62400050	p.N328S	2
chr11:62407103-62407103	p.C47R	2
chr11:62407174-62407174	p.L23fs*1	2
chr11:62406527-62406527	p.I103T	2
chr11:62400735-62400735	p.E213D	2
chr11:62406868-62406868	p.D72G	2
chr11:62396262-62396262	p.R720L	2

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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	7	6	1	12	2		2		2			8	4	4			4	3	1	6
# mutation	8	6	1	11	2		2		2			9	4	4			4	3	1	8
nonsynonymous SNV	4	3	1	9			1		1			6	4	2			4	1	1	8
synonymous SNV	4	3		2	2		1		1			3		2				2

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
chr11:62407103	p.E99E,GANAB	2
chr11:62400735	p.C47R,GANAB	2
chr11:62397917	p.H672Y,GANAB	1
chr11:62406541	p.M429I,GANAB	1
chr11:62394105	p.M179L,GANAB	1
chr11:62400106	p.V16F,GANAB	1
chr11:62396766	p.P610P,GANAB	1
chr11:62402314	p.A420P,GANAB	1
chr11:62397951	p.E174G,GANAB	1
chr11:62406547	p.R13R,GANAB	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 GANAB 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 GANAB

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


ATL3,DDB1,FEN1,GANAB,HNRNPUL2,HYOU1,INCENP, INTS5,EMC1,MARK2,MTA2,NAA40,NOMO1,OSBP, PATL1,PDIA4,RTN3,SKP2,STIP1,STT3A,TTC9C	PXYLP1,ALDH18A1,ARF3,ASTN2,CSTF2,DNAJC14,GANAB, HYOU1,IGSF3,KDM4A,MBTPS1,NIPSNAP1,ODF2,PDIA4, PI4KA,SEC16A,SND1,STT3A,SYT7,TM9SF4,TRIL

ARCN1,CKAP5,CPSF7,DDB1,GANAB,HSP90B1,HYOU1, INCENP,EMC1,LRP5,RNF121,RNF214,RNF26,SCYL1, SF1,SF3B2,SRPR,SSRP1,STIP1,STT3A,UGGT1	BMS1,CBX5,CKAP5,DCAF7,DDB1,GANAB,GCN1L1, HNRNPU,EMC1,VWA8,LARP1,LRBA,NUP214,PRKDC, PRPF8,SAFB2,SAFB,SF3B3,TAF15,UGGT1,VPRBP

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 GANAB

There's no related Drug.

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Cross referenced IDs for GANAB

* 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