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 SMG9

Basic gene info.	Gene symbol	SMG9
	Gene name	SMG9 nonsense mediated mRNA decay factor
	Synonyms	C19orf61\|F17127_1
	Cytomap	UCSC genome browser: 19q13.31
	Genomic location	chr19 :44235300-44259142
	Type of gene	protein-coding
	RefGenes	NM_019108.2,
	Ensembl id	ENSG00000105771
	Description	protein SMG9protein smg-9 homologsmg-9 homolog, nonsense mediated mRNA decay factor
	Modification date	20141207
dbXrefs	MIM : 613176
	HGNC : HGNC
	HPRD : 07800
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMG9
	BioGPS: 56006
	Gene Expression Atlas: ENSG00000105771
	The Human Protein Atlas: ENSG00000105771
Pathway	NCI Pathway Interaction Database: SMG9
	KEGG: SMG9
	REACTOME: SMG9
	ConsensusPathDB
	Pathway Commons: SMG9
Metabolism	MetaCyc: SMG9
	HUMANCyc: SMG9
Regulation	Ensembl's Regulation: ENSG00000105771
	miRBase: chr19 :44,235,300-44,259,142
	TargetScan: NM_019108
	cisRED: ENSG00000105771
Context	iHOP: SMG9
	cancer metabolism search in PubMed: SMG9
	UCL Cancer Institute: SMG9
Assigned class in ccmGDB	C

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Phenotypic Information for SMG9(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SMG9
	Familial Cancer Database: SMG9

* 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: SMG9
	MedGen: SMG9 (Human Medical Genetics with Condition)
	ClinVar: SMG9
Phenotype	MGI: SMG9 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SMG9

Mutations for SMG9

* 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	SMG9	chr19	44254119	44254139	SMG9	chr19	44255006	44255026

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 SMG9 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

BQ067678

SMG9

157

44258892

44259036

KDM1B

157

338

18212731

18213962

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=26)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=2)
There's no deleted 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
chr19:44254859-44254859	p.Y12C	3
chr19:44237020-44237020	p.E492K	3
chr19:44254883-44254883	p.S4C	2
chr19:44237872-44237872	p.N372K	2
chr19:44244370-44244370	p.R234S	2
chr19:44249017-44249017	p.D203G	1
chr19:44237094-44237094	p.Q467R	1
chr19:44251905-44251905	p.P124S	1
chr19:44242286-44242286	p.Y299Y	1
chr19:44254799-44254799	p.S32C	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	3	1		10			1		1			4	1				3	3		4
# mutation	3	1		8			1		1			4	1				3	3		4
nonsynonymous SNV	1	1		6			1					3	1				1	2		2
synonymous SNV	2			2					1			1					2	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
chr19:44254856	p.G13V	2
chr19:44251656	p.R176C	2
chr19:44251908	p.A123T	2
chr19:44254813	p.D327N	1
chr19:44237802	p.E38E	1
chr19:44251649	p.R287H	1
chr19:44237823	p.P28T	1
chr19:44254859	p.L282V	1
chr19:44241758	p.G27G	1
chr19:44251687	p.I278I	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 SMG9 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 SMG9

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


ATP5SL,SMG9,CCDC61,ERCC1,EXOSC5,GEMIN7,MYPOP, QPCTL,RBM42,RPS19,RPS19BP1,SDHAF1,SNRPD2,THAP3, TOMM40,TRAPPC6A,VASP,XRCC1,ZNF428,ZNF524,ZNF576	ARMC7,ASB6,SMG9,CC2D1A,DCAF15,DEAF1,FUK, FZR1,MAN1B1,MED22,NAT9,NDOR1,POLD1,REXO4, RIN1,RPUSD1,SLC12A9,TRAF2,TSC22D4,WDR46,ZNF282

BCAT2,BLOC1S3,SMG9,CLPTM1,CNOT3,EGLN2,ERF, GSK3A,IRF3,LIG1,NFKBIB,NUP62,PAF1,PPP5C, PRPF31,SUPT5H,SUV420H2,TRIM28,U2AF2,UBE2M,ZNF574	BRD2,SMG9,MMS22L,EXOSC10,ILF3,IPO9,MCM3, NAT10,NOLC1,NUP188,ODF2,PFAS,R3HDM1,RANGAP1, RBM19,RBM28,TCHP,TCOF1,TTC26,UBAP2L,XPO7

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 SMG9

There's no related Drug.

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Cross referenced IDs for SMG9

* 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