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 SMG1

Basic gene info.	Gene symbol	SMG1
	Gene name	SMG1 phosphatidylinositol 3-kinase-related kinase
	Synonyms	61E3.4\|ATX\|LIP
	Cytomap	UCSC genome browser: 16p12.3
	Genomic location	chr16 :18816174-18937726
	Type of gene	protein-coding
	RefGenes	NM_015092.4,
	Ensembl id	ENSG00000157106
	Description	PI-3-kinase-related kinase SMG-1lambda-interacting proteinlambda/iota protein kinase C-interacting proteinserine/threonine-protein kinase SMG1smg-1 homolog, phosphatidylinositol 3-kinase-related kinase
	Modification date	20141222
dbXrefs	MIM : 607032
	HGNC : HGNC
	Ensembl : ENSG00000157106
	HPRD : 06123
	Vega : OTTHUMG00000166900
Protein	UniProt: Q96Q15 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SMG1
	BioGPS: 23049
	Gene Expression Atlas: ENSG00000157106
	The Human Protein Atlas: ENSG00000157106
Pathway	NCI Pathway Interaction Database: SMG1
	KEGG: SMG1
	REACTOME: SMG1
	ConsensusPathDB
	Pathway Commons: SMG1
Metabolism	MetaCyc: SMG1
	HUMANCyc: SMG1
Regulation	Ensembl's Regulation: ENSG00000157106
	miRBase: chr16 :18,816,174-18,937,726
	TargetScan: NM_015092
	cisRED: ENSG00000157106
Context	iHOP: SMG1
	cancer metabolism search in PubMed: SMG1
	UCL Cancer Institute: SMG1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SMG1 in cancer cell metabolism	1. Cheung H, St Jean M, Beug S, Lejmi-Mrad R, LaCasse E, et al. (2011) SMG1 and NIK regulate apoptosis induced by Smac mimetic compounds. Cell death & disease 2: e146. go to article

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Phenotypic Information for SMG1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SMG1
	Familial Cancer Database: SMG1

* 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	607032; gene.
Orphanet
Disease	KEGG Disease: SMG1
	MedGen: SMG1 (Human Medical Genetics with Condition)
	ClinVar: SMG1
Phenotype	MGI: SMG1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SMG1

Mutations for SMG1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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 SMG1 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
BE842124	ACAA2	13	144	18	47313702	47317942	SMG1	137	409	16	18845615	18846340
AV652799	SMG1	1	131	16	18856751	18856881	CYP2C9	127	756	10	96740952	96748968
DA481995	SMG1	243	263	16	18937306	18937326	KPNA3	247	581	13	50306748	50366697
DB219627	BPTF	1	70	17	65944237	65944305	SMG1	62	546	16	18820944	18826827
DA571449	KCNC3	200	452	19	50821889	50822141	SMG1	453	744	16	18816846	18817139
BG769973	SMG1	2	270	16	18819376	18819646	COMMD1	265	294	2	62357034	62357063
BE771673	SMG1	184	367	16	18839866	18840049	DOCK3	353	376	3	50981954	50981977

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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=186)	Stat. for Synonymous SNVs (# total SNVs=81)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=3)

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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
chr16:18882777-18882777	p.E733E	6
chr16:18820900-18820900	p.A3655A	4
chr16:18845568-18845568	p.S2837S	3
chr16:18887699-18887699	p.H542R	3
chr16:18900862-18900862	p.L214L	3
chr16:18865172-18865172	p.M1497V	3
chr16:18853072-18853072	p.S2167P	3
chr16:18851200-18851200	p.S2251S	2
chr16:18823443-18823443	p.R3539L	2
chr16:18841598-18841598	p.V2958V	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=9

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	7	8	5	43	2		10	1	5	6	3	28	12	2			15	18	2	27
# mutation	7	8	5	38	2		10	1	5	6	3	28	14	2			14	23	2	50
nonsynonymous SNV	5	6	5	26	1		9	1	3	5	3	19	10	2			13	17	1	39
synonymous SNV	2	2		12	1		1		2	1		10	4				1	6	1	11

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
chr16:18882777	p.E737E	6
chr16:18937330	p.A78T	3
chr16:18887699	p.H546R	3
chr16:18908139	p.S12G	3
chr16:18853072	p.S2171P	3
chr16:18827724	p.R1980Q	2
chr16:18845568	p.G3103R	2
chr16:18853724	p.R70R	2
chr16:18826800	p.R2091H	2
chr16:18882778	p.S1907F	2

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 SMG1 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 SMG1

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


ASXL2,BIRC6,BOD1L1,CCNT1,CREBBP,DDI2,KIAA0430, LCOR,LOC100271836,MAP3K2,NBEAL1,NIPBL,RAPGEF6,REST, RIF1,RSC1A1,SCAF11,SMG1,SON,TNRC6A,ZNF81	ASH1L,ATG2B,BIRC6,BRWD1,GPATCH2L,CCNT1,CEP350, CEP97,CHD9,ICE1,EPG5,LCOR,KMT2C,RICTOR, RIF1,LTN1,SMCHD1,SMG1,VPS13A,XRN1,ZKSCAN8

ATXN1L,BIRC6,HECTD4,CRAMP1L,CREBBP,GLTSCR1L,KIAA0556, KIAA2026,LOC100271836,MDN1,KMT2A,PDPK1,PIKFYVE,RBBP6, SHPRH,SMG1,SPEN,SRRM2,TNRC6A,UBN1,ZNF646	ATAD2B,PRRC2C,BPTF,BTAF1,CHD7,CHD9,DICER1, GON4L,LOC100190986,KMT2B___KMT2D,KMT2C,MON2,NIPBL,NKTR, PIKFYVE,RBM33,SLTM,SMG1,THOC2,TRIM33,ZCCHC2

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 SMG1

There's no related Drug.

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Cross referenced IDs for SMG1

* 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