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 GANC
Basic gene info.Gene symbolGANC
Gene nameglucosidase, alpha; neutral C
Synonyms-
CytomapUCSC genome browser: 15q15.2
Genomic locationchr15 :42566365-42645864
Type of geneprotein-coding
RefGenesNM_001301409.1,
NM_001301410.1,NM_198141.2,
Ensembl idENSG00000214013
Descriptionneutral alpha-glucosidase C
Modification date20141207
dbXrefs MIM : 104180
HGNC : HGNC
HPRD : 00077
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GANC
BioGPS: 2595
Gene Expression Atlas: ENSG00000214013
The Human Protein Atlas: ENSG00000214013
PathwayNCI Pathway Interaction Database: GANC
KEGG: GANC
REACTOME: GANC
ConsensusPathDB
Pathway Commons: GANC
MetabolismMetaCyc: GANC
HUMANCyc: GANC
RegulationEnsembl's Regulation: ENSG00000214013
miRBase: chr15 :42,566,365-42,645,864
TargetScan: NM_001301409
cisRED: ENSG00000214013
ContextiHOP: GANC
cancer metabolism search in PubMed: GANC
UCL Cancer Institute: GANC
Assigned class in ccmGDBC

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Phenotypic Information for GANC(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GANC
Familial Cancer Database: GANC
* 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
KEGG_GALACTOSE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM

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

Mutations for GANC
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryGANCchr154260576242605782TMEM87Achr154250623042506250
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 GANC related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW572233GANC1387154264579042645864GANC84214154264570442645834

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

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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=47)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:42614213-42614213p.R430C2
chr15:42602943-42602943p.R319H2
chr15:42619578-42619578p.D480N2
chr15:42602622-42602622p.S288S2
chr15:42632010-42632010p.T663A2
chr15:42614179-42614179p.P418P2
chr15:42641615-42641615p.G818D1
chr15:42585003-42585003p.I134L1
chr15:42621565-42621565p.P521Q1
chr15:42631902-42631902p.E627K1

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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
# sample32 7  5 3 134  177 10
# mutation32 7  5 3 134  197 16
nonsynonymous SNV22 6  3 2 134   57 13
synonymous SNV1  1  2 1      14  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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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
chr15:42632035p.P703H2
chr15:42619578p.D480N2
chr15:42632908p.R671T2
chr15:42585003p.P521Q1
chr15:42631929p.S288S1
chr15:42641615p.I543I1
chr15:42614213p.E705K1
chr15:42566701p.E8K1
chr15:42621632p.E301D1
chr15:42632010p.G562W1

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 GANC 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 GANC

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

AQR,RHOV___CHP1,CTDSPL2,FRMD4B,GANC,INO80,LOC729082,
RFX7,RNF111,SLC12A6,SNAP23,SPG11,SYNE2,TCF12,
TJP1,TMEM87A,TMOD3,UBR1,ZNF106,ZNF280D,ZNF770
APC,APOOL,ATF7IP,CLASP1,DPP8,CCSER2,GANC,
HECTD1,HELZ,KIAA1109,KIAA2018,LOC729082,FAN1,MTR,
PCNX,TTBK2,TTC37,UBR2,USP24,ZDBF2,ZFYVE9

AP4E1,AQR,CLPX,DPP8,EIF2AK4,FAM98B,GANC,
INO80,IQGAP1,LOC729082,MTMR10,PPIP5K1,RTF1,SPG11,
TMEM87A,TMOD3,TRPM7,UBE3A,USP8,ZNF106,ZNF770
AIFM3,ASAP3,C1orf159,CAMK1D,CAPN3,CWH43,D2HGDH,
DHTKD1,ENGASE,NXPE2,FUK,GANC,KREMEN1,MRPS5,
PROM2,ARHGAP44,SH2B1,SIRT5,STEAP3,TMEM87A,ZNF808
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 GANC


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