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 ALG1
Basic gene info.Gene symbolALG1
Gene nameALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase
SynonymsCDG1K|HMAT1|HMT-1|HMT1|MT-1|Mat-1|hMat-1
CytomapUCSC genome browser: 16p13.3
Genomic locationchr16 :5121809-5137380
Type of geneprotein-coding
RefGenesNM_019109.4,
Ensembl idENSG00000033011
DescriptionGDP-Man:GlcNAc2-PP-dolichol mannosyltransferaseGDP-mannose-dolichol diphosphochitobiose mannosyltransferaseasparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase ho
Modification date20141219
dbXrefs MIM : 605907
HGNC : HGNC
HPRD : 10437
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALG1
BioGPS: 56052
Gene Expression Atlas: ENSG00000033011
The Human Protein Atlas: ENSG00000033011
PathwayNCI Pathway Interaction Database: ALG1
KEGG: ALG1
REACTOME: ALG1
ConsensusPathDB
Pathway Commons: ALG1
MetabolismMetaCyc: ALG1
HUMANCyc: ALG1
RegulationEnsembl's Regulation: ENSG00000033011
miRBase: chr16 :5,121,809-5,137,380
TargetScan: NM_019109
cisRED: ENSG00000033011
ContextiHOP: ALG1
cancer metabolism search in PubMed: ALG1
UCL Cancer Institute: ALG1
Assigned class in ccmGDBC

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Phenotypic Information for ALG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALG1
Familial Cancer Database: ALG1
* 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: ALG1
MedGen: ALG1 (Human Medical Genetics with Condition)
ClinVar: ALG1
PhenotypeMGI: ALG1 (International Mouse Phenotyping Consortium)
PhenomicDB: ALG1

Mutations for ALG1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 ALG1 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
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=14)
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
chr16:5129756-5129756p.E303E4
chr16:5128838-5128838p.R274H3
chr16:5129771-5129771p.D308D3
chr16:5123195-5123195p.Q110E2
chr16:5127458-5127458p.F184F2
chr16:5123243-5123243p.Y126N2
chr16:5125427-5125427p.F143F2
chr16:5128001-5128001p.H241H2
chr16:5123184-5123184p.K106I1
chr16:5130982-5130982p.I333V1

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21252 4    413  43 2
# mutation21252 3    213  33 3
nonsynonymous SNV21141 2     13  23 3
synonymous SNV  111 1    2    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
chr16:5129756p.E303E6
chr16:5125427p.R274H2
chr16:5128838p.F143F2
chr16:5125493p.R99Q1
chr16:5123163p.E251G1
chr16:5125503p.Y103H1
chr16:5131001p.L269P1
chr16:5123174p.G104R1
chr16:5127452p.L269L1
chr16:5132575p.K106I1

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 ALG1 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 ALG1

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

ABHD14A,ALG14,ANAPC13,ATP5G2,C12orf57,SMDT1,COX16,
COX7C,CYB561D2,DAD1,GABARAP,LAMTOR5,NDUFB1,NDUFC1,
NDUFV2,PIGH,RPF1,RWDD3,SLC44A3,TMEM59,YIPF1
AIDA,AIG1,ALG14,ARL2BP,ATP6V0E1,EMC7,TMEM230,
CYB5B,DCTN6,GTF3A,HACL1,LYRM1,MGC72080,MGST1,
RHOA,ST7,TMEM14C,UBE2E2,UBE2L3,UBXN8,VPS29

ALG14,ATP5C1,ATP5F1,ATP5J,COA6,COMMD8,COX7A2,
DPY30,GNG5,LAMTOR5,ITGB3BP,MRPL22,MRPL48,MRPS15,
NDUFB1,PSMA5,RBX1,RPL5,SEP15,TOMM22,UQCRQ
ALG14,ATP5C1,ATP5G3,ATPIF1,MPC1,C15orf48,MIEN1,
COA3,CLIC1,FAM118B,MLX,MRPL27,MRPS11,NDUFB9,
PDCD6,POLR2H,PPCS,TSG101,UQCR10,UQCRFS1,VPS25
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 ALG1


There's no related Drug.
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Cross referenced IDs for ALG1
* 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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