Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolSMG1
Gene nameSMG1 phosphatidylinositol 3-kinase-related kinase
Synonyms61E3.4|ATX|LIP
CytomapUCSC genome browser: 16p12.3
Genomic locationchr16 :18816174-18937726
Type of geneprotein-coding
RefGenesNM_015092.4,
Ensembl idENSG00000157106
DescriptionPI-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 date20141222
dbXrefs MIM : 607032
HGNC : HGNC
Ensembl : ENSG00000157106
HPRD : 06123
Vega : OTTHUMG00000166900
ProteinUniProt: Q96Q15
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMG1
BioGPS: 23049
Gene Expression Atlas: ENSG00000157106
The Human Protein Atlas: ENSG00000157106
PathwayNCI Pathway Interaction Database: SMG1
KEGG: SMG1
REACTOME: SMG1
ConsensusPathDB
Pathway Commons: SMG1
MetabolismMetaCyc: SMG1
HUMANCyc: SMG1
RegulationEnsembl's Regulation: ENSG00000157106
miRBase: chr16 :18,816,174-18,937,726
TargetScan: NM_015092
cisRED: ENSG00000157106
ContextiHOP: SMG1
cancer metabolism search in PubMed: SMG1
UCL Cancer Institute: SMG1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of SMG1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 607032; gene.
Orphanet
DiseaseKEGG Disease: SMG1
MedGen: SMG1 (Human Medical Genetics with Condition)
ClinVar: SMG1
PhenotypeMGI: SMG1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE842124ACAA213144184731370247317942SMG1137409161884561518846340
AV652799SMG11131161885675118856881CYP2C9127756109674095296748968
DA481995SMG1243263161893730618937326KPNA3247581135030674850366697
DB219627BPTF170176594423765944305SMG162546161882094418826827
DA571449KCNC3200452195082188950822141SMG1453744161881684618817139
BG769973SMG12270161881937618819646COMMD126529426235703462357063
BE771673SMG1184367161883986618840049DOCK335337635098195450981977

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr16:18882777-18882777p.E733E6
chr16:18820900-18820900p.A3655A4
chr16:18845568-18845568p.S2837S3
chr16:18865172-18865172p.M1497V3
chr16:18887699-18887699p.H542R3
chr16:18900862-18900862p.L214L3
chr16:18853072-18853072p.S2167P3
chr16:18849503-18849503p.A2412T2
chr16:18844477-18844477p.S2855S2
chr16:18861604-18861604p.L1742L2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample785432 10156328122  1518227
# mutation785382 10156328142  1423250
nonsynonymous SNV565261 9135319102  1317139
synonymous SNV22 121 1 21 104   16111
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr16:18882777p.E737E6
chr16:18937330p.A78T3
chr16:18887699p.H546R3
chr16:18908139p.S2171P3
chr16:18853072p.S12G3
chr16:18859259p.R70R2
chr16:18840904p.R3623L2
chr16:18827724p.C3401Y2
chr16:18845568p.K3583R2
chr16:18853724p.R1980Q2

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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