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 SMG6

Basic gene info.	Gene symbol	SMG6
	Gene name	SMG6 nonsense mediated mRNA decay factor
	Synonyms	C17orf31\|EST1A\|SMG-6\|hSMG5/7a
	Cytomap	UCSC genome browser: 17p13.3
	Genomic location	chr17 :1963132-1992055
	Type of gene	protein-coding
	RefGenes	NM_001256827.1, NM_001256828.1,NM_001282326.1,NM_017575.4,NM_001170957.1,
	Ensembl id	ENSG00000070366
	Description	EST1 telomerase component homolog Aever shorter telomeres 1Asmg-6 homolog, nonsense mediated mRNA decay factortelomerase subunit EST1Atelomerase-binding protein EST1A
	Modification date	20141207
dbXrefs	MIM : 610963
	HGNC : HGNC
	Ensembl : ENSG00000070366
	HPRD : 06502
	Vega : OTTHUMG00000177578
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMG6
	BioGPS: 23293
	Gene Expression Atlas: ENSG00000070366
	The Human Protein Atlas: ENSG00000070366
Pathway	NCI Pathway Interaction Database: SMG6
	KEGG: SMG6
	REACTOME: SMG6
	ConsensusPathDB
	Pathway Commons: SMG6
Metabolism	MetaCyc: SMG6
	HUMANCyc: SMG6
Regulation	Ensembl's Regulation: ENSG00000070366
	miRBase: chr17 :1,963,132-1,992,055
	TargetScan: NM_001256827
	cisRED: ENSG00000070366
Context	iHOP: SMG6
	cancer metabolism search in PubMed: SMG6
	UCL Cancer Institute: SMG6
Assigned class in ccmGDB	C

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Phenotypic Information for SMG6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SMG6
	Familial Cancer Database: SMG6

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: SMG6
	MedGen: SMG6 (Human Medical Genetics with Condition)
	ClinVar: SMG6
Phenotype	MGI: SMG6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SMG6

Mutations for SMG6

* 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

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

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 SMG6 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
DA746032	ZFP36L1	1	118	14	69261839	69261956	SMG6	116	563	17	1968369	1972227
BP250136	NPIPB7	1	382	16	28548976	28550333	SMG6	377	592	17	2057997	2058212
BP223879	SMG6	1	147	17	2113443	2113589	DSG2	147	661	18	29111160	29118801
BE837736	SMG6	1	292	17	2115708	2115998	ITFG2	284	483	12	2933402	2933601
BF733944	SMG6	14	229	17	2203163	2203379	TNRC6A	214	309	16	24802394	24802489

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=89)	Stat. for Synonymous SNVs (# total SNVs=30)

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
chr17:2203200-2203200	p.Q283*	3
chr17:2203453-2203453	p.A198A	2
chr17:2202449-2202449	p.G533D	2
chr17:2139842-2139842	p.R938H	2
chr17:2186958-2186958	p.K803K	2
chr17:2196207-2196207	p.R739Q	2
chr17:1989033-1989033	p.R1174*	2
chr17:2203334-2203334	p.P238L	2
chr17:2202208-2202208	p.A613A	2
chr17:1968908-1968908	p.R1301C	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	2	1	3	15			3		5			7	6	1		1	7	15	1	11
# mutation	2	1	3	16			3		5			7	6	1		1	8	16	1	15
nonsynonymous SNV	1	1	1	13			3		3			6	5	1			5	8		14
synonymous SNV	1		2	3					2			1	1			1	3	8	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
chr17:2203910	p.A613A	2
chr17:2202208	p.R402W	2
chr17:2202843	p.R46H	2
chr17:2203823	p.G437V	1
chr17:2089982	p.A192V	1
chr17:2202561	p.T208T,SMG6	1
chr17:2186977	p.R815W	1
chr17:2202976	p.Q657Q	1
chr17:2203419	p.P429S	1
chr17:1972199	p.G184E	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 SMG6 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 SMG6

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


ABR,ANKFY1,CTC1,C17orf85,CAMTA2,CHD3,CTNS, DPH1,KIAA0753,METTL16,MINK1,MNT,NEURL4,SGSM2, SHPK,SMG6,SMYD4,VPS53,WDR81,ZBTB4,ZZEF1	ALX3,ANKRD11,C22orf46,CEP250,CHD3,SPECC1L,DHX38, EXOC7,STRIP1,GLG1,IP6K1,LTBP3,NUMA1,PRR12, RBM19,SMG6,SUPT6H,TNRC18,UPF1,ZC3H7B,ZNF646

AHDC1,AKAP13,ANKFY1,CAMTA2,CTNS,FLII,FXR2, KDM6B,MNT,MPRIP,MYO1C,NCOR1,PAFAH1B1,POLR2A, PRPF8,RABEP1,RAI1,SMG6,WDR81,ZBTB4,ZNF407	PRRC2B,HECTD4,CHD8,CREBBP,DDX42,DYNC1H1,EP300, EP400,FAM193A,GLG1,HERC2,HUWE1,MED12,MED13L, NCOR2,NUMA1,SMG6,SNRNP200,SUPT6H,TNRC6C,ZNF407

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 SMG6

There's no related Drug.

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Cross referenced IDs for SMG6

* 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