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 FUT8

Basic gene info.	Gene symbol	FUT8
	Gene name	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)
	Synonyms	-
	Cytomap	UCSC genome browser: 14q24.3
	Genomic location	chr14 :65879447-66210839
	Type of gene	protein-coding
	RefGenes	NM_004480.4, NM_178155.2,NM_178156.2,NR_038167.1,NR_038170.1, NM_178154.1,NM_178157.1,
	Ensembl id	ENSG00000033170
	Description	GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1,6-fucosyltransferaseGDP-fucose--glycoprotein fucosyltransferasealpha-(1,6)-fucosyltransferasealpha1-6FucTglycoprotein 6-alpha-L-fucosyltransferase
	Modification date	20141207
dbXrefs	MIM : 602589
	HGNC : HGNC
	Ensembl : ENSG00000033170
	HPRD : 03994
	Vega : OTTHUMG00000142818
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FUT8
	BioGPS: 2530
	Gene Expression Atlas: ENSG00000033170
	The Human Protein Atlas: ENSG00000033170
Pathway	NCI Pathway Interaction Database: FUT8
	KEGG: FUT8
	REACTOME: FUT8
	ConsensusPathDB
	Pathway Commons: FUT8
Metabolism	MetaCyc: FUT8
	HUMANCyc: FUT8
Regulation	Ensembl's Regulation: ENSG00000033170
	miRBase: chr14 :65,879,447-66,210,839
	TargetScan: NM_004480
	cisRED: ENSG00000033170
Context	iHOP: FUT8
	cancer metabolism search in PubMed: FUT8
	UCL Cancer Institute: FUT8
Assigned class in ccmGDB	C

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Phenotypic Information for FUT8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: FUT8
	Familial Cancer Database: FUT8

* 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: FUT8
	MedGen: FUT8 (Human Medical Genetics with Condition)
	ClinVar: FUT8
Phenotype	MGI: FUT8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: FUT8

Mutations for FUT8

* 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

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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	FUT8	chr14	65880659	65880679	FUT8	chr14	65880891	65880911
ovary	FUT8	chr14	65914893	65914913	FUT8	chr14	65997088	65997108
ovary	FUT8	chr14	65940360	65940380	FUT8	chr14	65965283	65965303
ovary	FUT8	chr14	65940549	65940569	MAX	chr14	65490848	65490868
ovary	FUT8	chr14	66009894	66009914	FUT8	chr14	66201873	66201893
ovary	FUT8	chr14	66210535	66210555	FUT8	chr14	66210654	66210674
pancreas	FUT8	chr14	65907546	65907566	MAX	chr14	65542325	65542345
pancreas	FUT8	chr14	65968239	65968259	FUT8	chr14	65981297	65981317
pancreas	FUT8	chr14	66193680	66193700	FUT8	chr14	66155888	66155908

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 FUT8 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
AW361302	IFRD1	1	312	7	112112877	112115756	FUT8	298	656	14	66166618	66166979
BF996799	FUT8	33	302	14	66209024	66209298	IFT52	295	348	20	42232476	42232529

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=46)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr14:66209075-66209075	p.R559*	4
chr14:66208947-66208947	p.R516Q	3
chr14:66136173-66136173	p.S270S	3
chr14:66208906-66208906	p.Q502H	2
chr14:66136002-66136002	p.N213N	2
chr14:66200031-66200031	p.R448C	2
chr14:66028372-66028372	p.R31*	2
chr14:66136172-66136172	p.S270F	2
chr14:66028432-66028432	p.E51Q	2
chr14:66083023-66083023	p.K138N	2

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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=3

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	3			8			1		1			7	5	1		1	11	5		10
# mutation	3			6			1		1			7	6	1		1	11	5		10
nonsynonymous SNV	3			5			1		1			5	2	1			7	4		9
synonymous SNV				1								2	4			1	4	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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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
chr14:66136173	p.S107S,FUT8	3
chr14:66136172	p.T89A,FUT8	2
chr14:66208947	p.S107Y,FUT8	2
chr14:66083023	p.R353Q,FUT8	2
chr14:66136117	p.K138K,FUT8	2
chr14:66136158	p.D59N,FUT8	1
chr14:66200026	p.Q83H,FUT8	1
chr14:66028393	p.L289L,FUT8	1
chr14:66096228	p.A64A,FUT8	1
chr14:66209066	p.R86H,FUT8	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 FUT8 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 FUT8

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


ATP8B1,DCAF5,EXD2,EXOC6,FAM63A,FNTB,FOXA1, FUT8,LOC645431,NEK9,PGGT1B,PSEN1,RABEP1,RNF103, SEL1L,SLC19A2,SLC39A9,SPOPL,STAM2,TMEM30B,ZFYVE1	PXYLP1,AFF3,AP2B1,SAMD15,CHST15,COL4A5,DNAJC12, F2RL2,FTO,FUT8,IGSF3,KIAA1211,LRP2,MAGI3, PNMA2,SLC2A10,SYTL2,TANC2,THSD4,TPBG,TSPAN5

ARF6,TMEM263,MCU,CDC42EP1,EGLN3,ERO1L,FUT8, GNPNAT1,JKAMP,LOC645431,LPCAT1,PKM,PLEK2,RAB27B, RPL36AL,SCFD1,SEMA4B,SGMS1,SPTLC2,TC2N,TMED10	ACRBP,AIG1,AKR1A1,ATP6V1B2,BDH2,TMEM256,CRYZ, CTSH,FTL,FUT8,GATM,HACL1,HPS3,LIPA, LPO,MTHFS,PALB2,ECI2,PPAPDC1B,TFEC,TM2D2

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 FUT8

There's no related Drug.

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Cross referenced IDs for FUT8

* 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