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 ALG14

Basic gene info.	Gene symbol	ALG14
	Gene name	ALG14, UDP-N-acetylglucosaminyltransferase subunit
	Synonyms	-
	Cytomap	UCSC genome browser: 1p21.3
	Genomic location	chr1 :95448278-95538507
	Type of gene	protein-coding
	RefGenes	NM_144988.3,
	Ensembl id	ENSG00000172339
	Description	UDP-N-acetylglucosamine transferase subunit ALG14 homolog
	Modification date	20141207
dbXrefs	MIM : 612866
	HGNC : HGNC
	HPRD : 14466
Protein	UniProt: Q96F25 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALG14
	BioGPS: 199857
	Gene Expression Atlas: ENSG00000172339
	The Human Protein Atlas: ENSG00000172339
Pathway	NCI Pathway Interaction Database: ALG14
	KEGG: ALG14
	REACTOME: ALG14
	ConsensusPathDB
	Pathway Commons: ALG14
Metabolism	MetaCyc: ALG14
	HUMANCyc: ALG14
Regulation	Ensembl's Regulation: ENSG00000172339
	miRBase: chr1 :95,448,278-95,538,507
	TargetScan: NM_144988
	cisRED: ENSG00000172339
Context	iHOP: ALG14
	cancer metabolism search in PubMed: ALG14
	UCL Cancer Institute: ALG14
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ALG14(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ALG14
	Familial Cancer Database: ALG14

* 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	612866; gene.
Orphanet	353327; Congenital myasthenic syndromes with glycosylation defect.
Disease	KEGG Disease: ALG14
	MedGen: ALG14 (Human Medical Genetics with Condition)
	ClinVar: ALG14
Phenotype	MGI: ALG14 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALG14

Mutations for ALG14

* 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
haematopoietic_and_lymphoid_tissue	ALG14	chr1	95474122	95474122	ALG14	chr1	95474122	95474122
prostate	ALG14	chr1	95506321	95508321		chr2	159585322	159587322

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 ALG14 related fusion information.

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

DA767890

ALG14

308

95530421

95538473

LOC158435

307

719

98855307

98857548

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=14)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr1:95538398-95538398	p.I19I	2
chr1:95448642-95448642	p.R214Q	1
chr1:95492803-95492803	p.Y101C	1
chr1:95538408-95538408	p.V16G	1
chr1:95448643-95448643	p.R214R	1
chr1:95530462-95530462	p.S83Y	1
chr1:95538419-95538419	p.G12G	1
chr1:95448722-95448722	p.I187I	1
chr1:95530477-95530477	p.A78V	1
chr1:95538430-95538430	p.A9T	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		3					2			2	1	1			4	2		3
# mutation		1		3					2			2	1	1			3	2		3
nonsynonymous SNV		1		3					1			2					2	1		2
synonymous SNV									1				1	1			1	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
chr1:95538398	p.I19I	2
chr1:95448642	p.R27C	1
chr1:95530569	p.R214Q	1
chr1:95448643	p.R214R	1
chr1:95538365	p.G12G	1
chr1:95448750	p.V178A	1
chr1:95538368	p.A8P	1
chr1:95448777	p.I169T	1
chr1:95538372	p.L162P	1
chr1:95448798	p.K137T	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 ALG14 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 ALG14

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


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

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 ALG14

There's no related Drug.

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Cross referenced IDs for ALG14

* 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