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 ALG6
Basic gene info.Gene symbolALG6
Gene nameALG6, alpha-1,3-glucosyltransferase
SynonymsCDG1C
CytomapUCSC genome browser: 1p31.3
Genomic locationchr1 :63833260-63904233
Type of geneprotein-coding
RefGenesNM_013339.3,
Ensembl idENSG00000088035
DescriptionMan(9)GlcNAc(2)-PP-Dol alpha-1,3-glucosyltransferaseasparagine-linked glycosylation 6 homolog (S. cerevisiae, alpha-1,3-glucosyltransferase)asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)asparagine-linked glycosylation
Modification date20141219
dbXrefs MIM : 604566
HGNC : HGNC
Ensembl : ENSG00000088035
HPRD : 05194
Vega : OTTHUMG00000009140
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALG6
BioGPS: 29929
Gene Expression Atlas: ENSG00000088035
The Human Protein Atlas: ENSG00000088035
PathwayNCI Pathway Interaction Database: ALG6
KEGG: ALG6
REACTOME: ALG6
ConsensusPathDB
Pathway Commons: ALG6
MetabolismMetaCyc: ALG6
HUMANCyc: ALG6
RegulationEnsembl's Regulation: ENSG00000088035
miRBase: chr1 :63,833,260-63,904,233
TargetScan: NM_013339
cisRED: ENSG00000088035
ContextiHOP: ALG6
cancer metabolism search in PubMed: ALG6
UCL Cancer Institute: ALG6
Assigned class in ccmGDBC

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Phenotypic Information for ALG6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALG6
Familial Cancer Database: ALG6
* 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: ALG6
MedGen: ALG6 (Human Medical Genetics with Condition)
ClinVar: ALG6
PhenotypeMGI: ALG6 (International Mouse Phenotyping Consortium)
PhenomicDB: ALG6

Mutations for ALG6
* 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
ovaryALG6chr16389495863894978ALG6chr16389606563896085
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 ALG6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP430141ALG6735616383654363868001GNAS354415205748611157486172
BI493648ALG6814616390273463902872SMURF114755679869683498697268

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 # sample      1        1 
GAIN (# sample)               1 
LOSS (# sample)      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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
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
chr1:63876940-63876940p.H206H4
chr1:63876980-63876980p.K220*2
chr1:63877657-63877657p.L247L2
chr1:63902566-63902566p.P467S2
chr1:63872018-63872018p.P126R2
chr1:63872050-63872050p.E137*1
chr1:63902669-63902669p.R501I1
chr1:63862189-63862189p.G30C1
chr1:63881568-63881568p.L309L1
chr1:63872070-63872070p.K143N1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1116  2 1 112   42 5
# mutation1116  2 1 112   42 5
nonsynonymous SNV1114  2 1 112   31 4
synonymous SNV   2            11 1
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
chr1:63876858p.H206H1
chr1:63881568p.V275L1
chr1:63862189p.G30C1
chr1:63876877p.K289Q1
chr1:63894423p.Y38D1
chr1:63862213p.L292F1
chr1:63876887p.R42I1
chr1:63894444p.R294C1
chr1:63862226p.Y72H1
chr1:63876912p.H295N1

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 ALG6 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 ALG6

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

ALG6,ATG4C,BTF3L4,COA7,CDC7,DBF4,DEPDC1,
FAF1,GLMN,ITGB3BP,LRRC8B,MAGOH,NRD1,OMA1,
PRPF38A,RBBP4,SASS6,SERBP1,STIL,TTC4,USP1
ABI1,ACTR6,ALG6,API5,ARFIP1,C12orf29,C5orf28,
SMIM15,CAAP1,MRPL42,NUS1,NXT2,PGGT1B,RAB14,
RNF2,SCAMP1,SCOC,SERP1,TIPRL,TMEM33,UBA3

ABCD3,AK2,ALG14,ALG6,ATG4C,ATP5F1,BCAS2,
DEPDC1,EIF2B3,FPGT,GLMN,ITGB3BP,LRRC40,MRPL37,
OMA1,PRPF38A,PSMA5,RPAP2,RPF1,RTCA,SERBP1
ALG6,CNOT11,SMIM15,CAAP1,DTWD2,ESRP1,FAR2,
FASTKD1,GRSF1,MRRF,AP5M1,NARS,NECAP1,PGGT1B,
PIGA,PPIP5K2,PRPF40A,SACM1L,SLC30A9,SRPK1,STARD7
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 ALG6


There's no related Drug.
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Cross referenced IDs for ALG6
* 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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