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 STT3A

Basic gene info.	Gene symbol	STT3A
	Gene name	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)
	Synonyms	ITM1\|STT3-A\|TMC
	Cytomap	UCSC genome browser: 11q23.3
	Genomic location	chr11 :125462738-125491280
	Type of gene	protein-coding
	RefGenes	NM_001278503.1, NM_001278504.1,NM_152713.4,
	Ensembl id	ENSG00000134910
	Description	B5STT3, subunit of the oligosaccharyltransferase complex, homolog ASTT3A, cataylic subunit of the oligosaccharyltransferase complexdolichyl-diphosphooligosaccharide protein glycotransferasedolichyl-diphosphooligosaccharide--protein glycosyltransferase
	Modification date	20141219
dbXrefs	MIM : 601134
	HGNC : HGNC
	Ensembl : ENSG00000134910
	HPRD : 03086
	Vega : OTTHUMG00000165852
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_STT3A
	BioGPS: 3703
	Gene Expression Atlas: ENSG00000134910
	The Human Protein Atlas: ENSG00000134910
Pathway	NCI Pathway Interaction Database: STT3A
	KEGG: STT3A
	REACTOME: STT3A
	ConsensusPathDB
	Pathway Commons: STT3A
Metabolism	MetaCyc: STT3A
	HUMANCyc: STT3A
Regulation	Ensembl's Regulation: ENSG00000134910
	miRBase: chr11 :125,462,738-125,491,280
	TargetScan: NM_001278503
	cisRED: ENSG00000134910
Context	iHOP: STT3A
	cancer metabolism search in PubMed: STT3A
	UCL Cancer Institute: STT3A
Assigned class in ccmGDB	C

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Phenotypic Information for STT3A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: STT3A
	Familial Cancer Database: STT3A

* 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: STT3A
	MedGen: STT3A (Human Medical Genetics with Condition)
	ClinVar: STT3A
Phenotype	MGI: STT3A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: STT3A

Mutations for STT3A

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows STT3A 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
EC545946	STT3A	1	66	11	125488308	125488374	CKB	59	103	14	103986331	103986376
AU139929	STT3A	1	287	11	125462749	125472235	LIPG	280	654	18	47091715	47095841
BE696961	STT3A	17	88	11	125462999	125463073	GJA1	81	187	6	121769334	121769440
CN404588	STT3A	1	270	11	125463926	125464195	LRRC47	268	609	1	3696902	3697243
BE837748	STT3A	52	194	11	125474050	125475574	UBQLN4	183	499	1	156013163	156013479
BF803158	STT3A	22	292	11	125490436	125490703	PTPN23	273	433	3	47450292	47450452
AW366596	CARKD	278	338	13	111290474	111290534	STT3A	339	462	11	125474095	125475599
AW366584	CARKD	245	305	13	111290474	111290534	STT3A	306	429	11	125474095	125475599

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=2

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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=10)

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
chr11:125474106-125474106	p.I158V	2
chr11:125488267-125488267	p.?	2
chr11:125488282-125488282	p.L597I	2
chr11:125481361-125481361	p.R386W	2
chr11:125483055-125483055	p.R513C	2
chr11:125482500-125482500	p.L408P	2
chr11:125466960-125466960	p.S32Y	1
chr11:125478126-125478126	p.S301S	1
chr11:125484329-125484329	p.?	1
chr11:125479493-125479493	p.?	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	4			1		3			8	4			1	6	6	2	10
# mutation	1		1	4			1		3			11	4			1	6	6	2	13
nonsynonymous SNV	1		1	4					3			8	2			1	1	5	1	10
synonymous SNV							1					3	2				5	1	1	3

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
chr11:125488282	p.L505I,STT3A	2
chr11:125466960	p.R75Q,STT3A	1
chr11:125481355	p.H175Y,STT3A	1
chr11:125475575	p.L316P,STT3A	1
chr11:125483032	p.E522E,STT3A	1
chr11:125478128	p.A76A,STT3A	1
chr11:125472242	p.F207F,STT3A	1
chr11:125481361	p.R345H,STT3A	1
chr11:125475577	p.L80L,STT3A	1
chr11:125484098	p.S209S,STT3A	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 STT3A 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 STT3A

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


ALG9,ARCN1,C11orf57,CHEK1,DDX10,DDX6,DLAT, DPAGT1,EI24,HYOU1,PUS3,RBM7,REXO2,RNF214, SDHD,SRPR,STT3A,UBE4A,USP28,ZPR1,ZW10	ACTL6A,ALDH18A1,AP2B1,B3GALNT1,RHNO1,VWA9,CASP2, GANAB,HSP90B1,PDIA3,PDIA3P1,RBBP4,RDH11,SEC23B, SHQ1,SLC39A9,STT3A,TCTN1,TCTN3,TM9SF2,XRCC5

ALG9,ARCN1,CANX,CHEK1,DPAGT1,EI24,FEN1, GANAB,HSP90B1,HYOU1,LOC653566,NCAPD3,OSBP,POLD3, SPCS2,SSR1,SSRP1,STIP1,STT3A,USP28,ZW10	ASCC3,ATAD2,BUB1B,CAPRIN1,DPAGT1,DTL,HSP90B1, HYOU1,LMNB1,MESDC2,MTHFD1,PDIA4,RPN2,RRM1, SCFD2,SEC61A1,SND1,SSRP1,STT3A,STT3B,UGGT1

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 STT3A

There's no related Drug.

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Cross referenced IDs for STT3A

* 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