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 symbolGANAB
Gene nameglucosidase, alpha; neutral AB
SynonymsG2AN|GLUII
CytomapUCSC genome browser: 11q12.3
Genomic locationchr11 :62392299-62414104
Type of geneprotein-coding
RefGenesNM_014610.3,
NM_001278192.1,NM_001278193.1,NM_001278194.1,NM_198334.2,
NM_198335.3,
Ensembl idENSG00000089597
DescriptionHEL-S-164nAalpha glucosidase II alpha subunitalpha-glucosidase 2epididymis secretory sperm binding protein Li 164nAglucosidase II subunit alphaneutral alpha-glucosidase AB
Modification date20141207
dbXrefs MIM : 104160
HGNC : HGNC
Ensembl : ENSG00000089597
HPRD : 03516
Vega : OTTHUMG00000167696
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GANAB
BioGPS: 23193
Gene Expression Atlas: ENSG00000089597
The Human Protein Atlas: ENSG00000089597
PathwayNCI Pathway Interaction Database: GANAB
KEGG: GANAB
REACTOME: GANAB
ConsensusPathDB
Pathway Commons: GANAB
MetabolismMetaCyc: GANAB
HUMANCyc: GANAB
RegulationEnsembl's Regulation: ENSG00000089597
miRBase: chr11 :62,392,299-62,414,104
TargetScan: NM_014610
cisRED: ENSG00000089597
ContextiHOP: GANAB
cancer metabolism search in PubMed: GANAB
UCL Cancer Institute: GANAB
Assigned class in ccmGDBC

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Phenotypic Information for GANAB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GANAB
MedGen: GANAB (Human Medical Genetics with Condition)
ClinVar: GANAB
PhenotypeMGI: GANAB (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GANAB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA340619RAMP112472238768266238786006GANAB244583116240645962407205
AK295899RAMP112462238768266238786006GANAB2433424116239290462407205
DB067719TRAF61230113653159636531822GANAB228465116240656062407204
AI339818ASNA110192191285895512859137GANAB193284116239248862392579
DW439793RPL1818114194911998649120082GANAB114189116239230562392381
BF085691GANAB1274116240892562408987STX7681756132824675132834200
BF514651RPS61733091937625319378387GANAB329405116240692862407163
BF987702GANAB1190116239306062393248GANAB178432116239451762396350
BE710656GANAB14111116239276262392861GANAB107296116239295262393141
AA557976GANAB7114116239273662392843GANAB112357116239284162393086
BF893584GRM81712047126524936126524998GANAB204463116239248662393205
BE773523PRKCSH162191155709811557160GANAB55159116240730762407411

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 # sample1                
GAIN (# sample)1                
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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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=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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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
chr11:62396762-62396762p.V614M3
chr11:62407101-62407101p.C47C2
chr11:62400658-62400658p.Y239C2
chr11:62400050-62400050p.N328S2
chr11:62407103-62407103p.C47R2
chr11:62407174-62407174p.L23fs*12
chr11:62406527-62406527p.I103T2
chr11:62400735-62400735p.E213D2
chr11:62406868-62406868p.D72G2
chr11:62396262-62396262p.R720L2

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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
# sample761122 2 2  844  4316
# mutation861112 2 2  944  4318
nonsynonymous SNV4319  1 1  642  4118
synonymous SNV43 22 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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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
chr11:62407103p.E99E,GANAB2
chr11:62400735p.C47R,GANAB2
chr11:62394094p.P610P,GANAB1
chr11:62400063p.A420P,GANAB1
chr11:62396762p.E174G,GANAB1
chr11:62400959p.R13R,GANAB1
chr11:62397917p.R606L,GANAB1
chr11:62406541p.C388C,GANAB1
chr11:62394105p.R164P,GANAB1
chr11:62400106p.D25N,GANAB1

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 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

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

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
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 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



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