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 ALG5
Basic gene info.Gene symbolALG5
Gene nameALG5, dolichyl-phosphate beta-glucosyltransferase
SynonymsbA421P11.2
CytomapUCSC genome browser: 13q13.3
Genomic locationchr13 :37523907-37573504
Type of geneprotein-coding
RefGenesNM_001142364.1,
NM_013338.4,
Ensembl idENSG00000120697
DescriptionAlg5, S. cerevisiae, homolog ofasparagine-linked glycosylation 5 homolog (S. cerevisiae, dolichyl-phosphate beta-glucosyltransferase)asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)asparagine-linked glycosy
Modification date20141207
dbXrefs MIM : 604565
HGNC : HGNC
Ensembl : ENSG00000120697
HPRD : 05193
Vega : OTTHUMG00000016741
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ALG5
BioGPS: 29880
Gene Expression Atlas: ENSG00000120697
The Human Protein Atlas: ENSG00000120697
PathwayNCI Pathway Interaction Database: ALG5
KEGG: ALG5
REACTOME: ALG5
ConsensusPathDB
Pathway Commons: ALG5
MetabolismMetaCyc: ALG5
HUMANCyc: ALG5
RegulationEnsembl's Regulation: ENSG00000120697
miRBase: chr13 :37,523,907-37,573,504
TargetScan: NM_001142364
cisRED: ENSG00000120697
ContextiHOP: ALG5
cancer metabolism search in PubMed: ALG5
UCL Cancer Institute: ALG5
Assigned class in ccmGDBC

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Phenotypic Information for ALG5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ALG5
Familial Cancer Database: ALG5
* 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: ALG5
MedGen: ALG5 (Human Medical Genetics with Condition)
ClinVar: ALG5
PhenotypeMGI: ALG5 (International Mouse Phenotyping Consortium)
PhenomicDB: ALG5

Mutations for ALG5
* 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
* 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
ovaryALG5chr133754554437545564ALG5chr133754579837545818
ovaryALG5chr133756874437568764chr1221362755221362775
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 ALG5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
HM245395PIGU1230203320384633225710ALG5218616133752410737546195
HM245394ALG51272133755976437567805PIGU273750203316299733176411
BF815383ALG54306133752409537539828PRKCA306486176452479864524978

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=31)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr13:37569565-37569565p.R79W3
chr13:37524129-37524129p.R309*3
chr13:37563723-37563723p.?2
chr13:37546148-37546148p.S196C2
chr13:37569724-37569724p.V26I2
chr13:37569725-37569725p.I25I2
chr13:37563666-37563666p.V134V2
chr13:37526712-37526712p.Y266Y1
chr13:37569679-37569679p.E41K1
chr13:37539850-37539850p.R212H1

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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
# sample11 5  1 1   3   62 3
# mutation11 4  1 1   3   62 2
nonsynonymous SNV 1 3  1 1   2   21 1
synonymous SNV1  1        1   41 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
chr13:37569724p.V26I,ALG52
chr13:37569725p.I25I,ALG52
chr13:37539735p.G200G,ALG51
chr13:37569629p.L8L,ALG51
chr13:37539757p.R182H,ALG51
chr13:37569662p.I129I,ALG51
chr13:37539795p.S124Y,ALG51
chr13:37569684p.I117N,ALG51
chr13:37539850p.Y97Y,ALG51
chr13:37569720p.Q115E1

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 ALG5 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 ALG5

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

ALG5,SPRYD7,CNGA2,DHRS12,MICU2,EXOSC8,SUPT20H,
GABRQ,GTF3A,INTS6,LNX2,MRPS31,MTIF3,OR5K3,
POLR1D,RFXAP,RNASEH2B,SAP18,THSD1P1,UFM1,UTP14C
ALG5,ATP6V0E1,C18orf32,C1GALT1C1,CDC42,CETN2,DAD1,
DERL2,MYL12B,ORMDL2,POLR2K,PPCS,PRR13,PSMD10,
SFT2D1,SNRPB2,TMCO1,TMEM59,TSPAN31,TXNDC12,WDR61

ABHD13,ALG5,MZT1,EXOSC8,HMGB1,GPALPP1,MED4,
MRPL57,MRPS31,MTRF1,NDFIP2,NUFIP1,PCID2,PIBF1,
RNASEH2B,SAP18,TGDS,TPT1,UBAC2,UCHL3,UFM1
ALG5,C14orf119,COA6,CCNC,CKLF,DPM1,GLRX3,
LAMTOR5,HSBP1,MED31,MRPL32,MRPS23,OSTC,PHF5A,
SELT,SEP15,TMEM126A,TMEM165,TOMM5,TOMM6,WDR61
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 ALG5


There's no related Drug.
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Cross referenced IDs for ALG5
* 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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