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 ALG9
Basic gene info.Gene symbolALG9
Gene nameALG9, alpha-1,2-mannosyltransferase
SynonymsCDG1L|DIBD1|LOH11CR1J
CytomapUCSC genome browser: 11q23
Genomic locationchr11 :111652918-111742004
Type of geneprotein-coding
RefGenesNM_001077690.1,
NM_001077691.1,NM_001077692.1,NM_024740.2,
Ensembl idENSG00000262577
Descriptionalpha-1,2-mannosyltransferase ALG9asparagine-linked glycosylation 9 homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)asparagine-linked glycosylation 9 homolog (yeast, alpha- 1,2-mannosyltransferase)asparagine-linked glycosylation 9, alpha-1,2-man
Modification date20141219
dbXrefs MIM : 606941
HGNC : HGNC
Ensembl : ENSG00000086848
HPRD : 09504
Vega : OTTHUMG00000166819
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALG9
BioGPS: 79796
Gene Expression Atlas: ENSG00000262577
The Human Protein Atlas: ENSG00000262577
PathwayNCI Pathway Interaction Database: ALG9
KEGG: ALG9
REACTOME: ALG9
ConsensusPathDB
Pathway Commons: ALG9
MetabolismMetaCyc: ALG9
HUMANCyc: ALG9
RegulationEnsembl's Regulation: ENSG00000262577
miRBase: chr11 :111,652,918-111,742,004
TargetScan: NM_001077690
cisRED: ENSG00000262577
ContextiHOP: ALG9
cancer metabolism search in PubMed: ALG9
UCL Cancer Institute: ALG9
Assigned class in ccmGDBC

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Phenotypic Information for ALG9(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALG9
Familial Cancer Database: ALG9
* 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: ALG9
MedGen: ALG9 (Human Medical Genetics with Condition)
ClinVar: ALG9
PhenotypeMGI: ALG9 (International Mouse Phenotyping Consortium)
PhenomicDB: ALG9

Mutations for ALG9
* 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
ovaryALG9chr11111659954111659974ALG9chr11111660033111660053
pancreasALG9chr11111729663111729683DLATchr11111904424111904444
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 ALG9 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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        
GAIN (# sample)                 
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=21)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr11:111711514-111711514p.P175L3
chr11:111724116-111724116p.G123G3
chr11:111708222-111708222p.R310*3
chr11:111680410-111680410p.E393K2
chr11:111724133-111724133p.V118I2
chr11:111708264-111708264p.E296*1
chr11:111724365-111724365p.?1
chr11:111708285-111708285p.P289S1
chr11:111711519-111711519p.G173G1
chr11:111724370-111724370p.?1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 10  2 21 531  51 5
# mutation12 6  2 21 531  51 5
nonsynonymous SNV12 3  1  1 321  41 3
synonymous SNV   3  1 2  21   1  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
chr11:111724116p.G123G,ALG94
chr11:111711514p.P175Q,ALG93
chr11:111739396p.R112C,ALG92
chr11:111680410p.E393Q,ALG92
chr11:111711524p.W77L,ALG91
chr11:111739391p.I366I,ALG91
chr11:111680426p.D69N,ALG91
chr11:111715419p.T345T,ALG91
chr11:111680489p.V169V,ALG91
chr11:111715427p.P318T,ALG91

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 ALG9 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 ALG9

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

AASDHPPT,ALG9,ARCN1,C11orf1,C11orf57,CUL5,CWF19L2,
DDX10,DDX6,DLAT,DPAGT1,EI24,EXPH5,FDXACB1,
NPAT,RNF214,SDHD,STT3A,UBE4A,USP28,ZW10
ALG9,TMEM230,CAV1,CAV2,CYB5B,DDHD2,EHHADH,
FAM45A,FBXL5,HRASLS5,SLC25A51,MGST1,MMD,PPP2R5A,
RTN3,SAR1A,SEC22B,SLC25A16,STX7,TEX261,TMEM135

AASDHPPT,ALG9,ALKBH8,BUD13,C11orf57,CCDC15,CEP57,
CUL5,CWC15,DDX10,DPAGT1,EI24,LOC653566,MRE11A,
PPP2R1B,RTN3,SPCS2,STT3A,UBE4A,USP28,ZW10
ALG9,ARIH1,KANSL1L,C3orf58,CLCC1,DCAF10,FXR1,
LRRC58,MTAP,MTR,NUP133,PCDHGA9,PCM1,PCYOX1,
PREPL,SEC63,TCF12,TOMM70A,TOP2B,UBQLN2,WDR82
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 ALG9


There's no related Drug.
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Cross referenced IDs for ALG9
* 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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