Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 ALG5

Basic gene info.	Gene symbol	ALG5
	Gene name	ALG5, dolichyl-phosphate beta-glucosyltransferase
	Synonyms	bA421P11.2
	Cytomap	UCSC genome browser: 13q13.3
	Genomic location	chr13 :37523907-37573504
	Type of gene	protein-coding
	RefGenes	NM_001142364.1, NM_013338.4,
	Ensembl id	ENSG00000120697
	Description	Alg5, 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 date	20141207
dbXrefs	MIM : 604565
	HGNC : HGNC
	Ensembl : ENSG00000120697
	HPRD : 05193
	Vega : OTTHUMG00000016741
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALG5
	BioGPS: 29880
	Gene Expression Atlas: ENSG00000120697
	The Human Protein Atlas: ENSG00000120697
Pathway	NCI Pathway Interaction Database: ALG5
	KEGG: ALG5
	REACTOME: ALG5
	ConsensusPathDB
	Pathway Commons: ALG5
Metabolism	MetaCyc: ALG5
	HUMANCyc: ALG5
Regulation	Ensembl's Regulation: ENSG00000120697
	miRBase: chr13 :37,523,907-37,573,504
	TargetScan: NM_001142364
	cisRED: ENSG00000120697
Context	iHOP: ALG5
	cancer metabolism search in PubMed: ALG5
	UCL Cancer Institute: ALG5
Assigned class in ccmGDB	C

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Phenotypic Information for ALG5(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ALG5
	MedGen: ALG5 (Human Medical Genetics with Condition)
	ClinVar: ALG5
Phenotype	MGI: ALG5 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ALG5	chr13	37545544	37545564	ALG5	chr13	37545798	37545818
ovary	ALG5	chr13	37568744	37568764		chr1	221362755	221362775

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ALG5 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
HM245395	PIGU	1	230	20	33203846	33225710	ALG5	218	616	13	37524107	37546195
HM245394	ALG5	1	272	13	37559764	37567805	PIGU	273	750	20	33162997	33176411
BF815383	ALG5	4	306	13	37524095	37539828	PRKCA	306	486	17	64524798	64524978

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr13:37569565-37569565	p.R79W	3
chr13:37524129-37524129	p.R309*	3
chr13:37546148-37546148	p.S196C	2
chr13:37569724-37569724	p.V26I	2
chr13:37569725-37569725	p.I25I	2
chr13:37563666-37563666	p.V134V	2
chr13:37563723-37563723	p.?	2
chr13:37567800-37567800	p.P99S	1
chr13:37539757-37539757	p.R243L	1
chr13:37559828-37559828	p.G166A	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		5			1		1				3				6	2		3
# mutation	1	1		4			1		1				3				6	2		2
nonsynonymous SNV		1		3			1		1				2				2	1		1
synonymous SNV	1			1									1				4	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr13:37569724	p.V26I,ALG5	2
chr13:37569725	p.I25I,ALG5	2
chr13:37569720	p.I117N,ALG5	1
chr13:37559848	p.Y97Y,ALG5	1
chr13:37559864	p.Q115E	1
chr13:37563628	p.V107L	1
chr13:37573378	p.P99S	1
chr13:37524105	p.P57P,ALG5	1
chr13:37563687	p.L287F,ALG5	1
chr13:37573414	p.F46L,ALG5	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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