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 SMG7

Basic gene info.	Gene symbol	SMG7
	Gene name	SMG7 nonsense mediated mRNA decay factor
	Synonyms	C1orf16\|EST1C\|SGA56M
	Cytomap	UCSC genome browser: 1q25
	Genomic location	chr1 :183441505-183523328
	Type of gene	protein-coding
	RefGenes	NM_001174061.1, NM_173156.2,NM_201568.2,NM_201569.2,NM_014837.3,
	Ensembl id	ENSG00000116698
	Description	EST1 telomerase component homolog CEST1-like protein Cbreast cancer-associated antigen SGA-56Mever shorter telomeres 1Cprotein SMG7smg-7 homolog, nonsense mediated mRNA decay factor
	Modification date	20141207
dbXrefs	MIM : 610964
	HGNC : HGNC
	Ensembl : ENSG00000116698
	HPRD : 10723
	Vega : OTTHUMG00000035221
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMG7
	BioGPS: 9887
	Gene Expression Atlas: ENSG00000116698
	The Human Protein Atlas: ENSG00000116698
Pathway	NCI Pathway Interaction Database: SMG7
	KEGG: SMG7
	REACTOME: SMG7
	ConsensusPathDB
	Pathway Commons: SMG7
Metabolism	MetaCyc: SMG7
	HUMANCyc: SMG7
Regulation	Ensembl's Regulation: ENSG00000116698
	miRBase: chr1 :183,441,505-183,523,328
	TargetScan: NM_001174061
	cisRED: ENSG00000116698
Context	iHOP: SMG7
	cancer metabolism search in PubMed: SMG7
	UCL Cancer Institute: SMG7
Assigned class in ccmGDB	C

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Phenotypic Information for SMG7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SMG7
	Familial Cancer Database: SMG7

* 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: SMG7
	MedGen: SMG7 (Human Medical Genetics with Condition)
	ClinVar: SMG7
Phenotype	MGI: SMG7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SMG7

Mutations for SMG7

* 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
pancreas	SMG7	chr1	183448375	183448395		chr1	183425116	183425136
pancreas	SMG7	chr1	183448377	183448397		chr1	183425116	183425136

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 SMG7 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
BF872191	SMG7	1	171	1	183457369	183457540	HNRNPF	164	302	10	43885934	43886072
AA598525	SMG7	1	338	1	183522990	183523326	SMG7	335	478	1	183522874	183523017
H80346	SMG7	1	29	1	183463921	183463949	FBXL20	13	288	17	37525934	37526469
BI014023	CDK13	11	313	7	40042752	40043102	SMG7	299	508	1	183512092	183512301

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=71)	Stat. for Synonymous SNVs (# total SNVs=25)

Stat. for Deletions (# total SNVs=5)	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
chr1:183495729-183495729	p.?	7
chr1:183502837-183502837	p.C345R	4
chr1:183520210-183520210	p.S1062L	3
chr1:183498545-183498545	p.V240V	2
chr1:183515224-183515224	p.E832Q	2
chr1:183520952-183520952	p.?	2
chr1:183510179-183510179	p.R452R	2
chr1:183515267-183515267	p.M849fs*1	2
chr1:183498593-183498593	p.F256F	2
chr1:183515287-183515287	p.P853S	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=4

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	2		14	3		2		2			9	10	2		1	11	2	1	14
# mutation	4	2		12	3		2		2			10	10	2		1	11	2	1	16
nonsynonymous SNV	4	1		9	1		1		2			9	9	1		1	9	2	1	12
synonymous SNV		1		3	2		1					1	1	1			2			4

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
chr1:183502837	p.C303R,SMG7	4
chr1:183520990	p.S755S,SMG7	1
chr1:183502377	p.P993P,SMG7	1
chr1:183514137	p.L84F,SMG7	1
chr1:183510179	p.H361P,SMG7	1
chr1:183515342	p.K560T,SMG7	1
chr1:183495796	p.Y778F,SMG7	1
chr1:183511600	p.D1003N,SMG7	1
chr1:183519030	p.K90K,SMG7	1
chr1:183502380	p.E362E,SMG7	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 SMG7 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 SMG7

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


AHCTF1,PRRC2C,SPRTN,BROX,SUCO,CAMSAP2,CDC73, CEP350,DHX9,FAM20B,FLVCR1,IPO9,RAB3GAP2,RBBP5, SLC25A44,SMG7,STX6,TADA1,TOR1AIP2,TPR,TROVE2	ARID2,PRR14L,CNOT1,AGO1,HEATR1,MGA,NF1, RNF111,SMG7,STX17,TNKS,TUG1,ZMYM4,ZKSCAN8, ZNF253,ZNF420,ZNF510,ZNF585A,ZNF616,ZNF623,ZNF81

ARHGEF11,ASH1L,PRRC2C,BCL9,CEP350,GON4L,HEATR1, LPGAT1,MTR,NCOA6,POGK,RAB3GAP2,RPRD2,SETDB1, SMG7,STX6,TP53BP2,UBAP2L,UBE2Q1,ZC3H11A,ZNF687	AKAP13,BIRC6,CDK13,FOXJ3,FOXO3B,GBF1,GOLGB1, IGF2R,KDM2A,NCOR1,NF1,NIPBL,RALGAPB,SMG7, SON,SPEN,TNRC6B,UBN1,UBR4,UPF1,USP9X

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 SMG7

There's no related Drug.

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Cross referenced IDs for SMG7

* 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