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 SAMM50
Basic gene info.Gene symbolSAMM50
Gene nameSAMM50 sorting and assembly machinery component
SynonymsOMP85|SAM50|TOB55|TRG-3|YNL026W
CytomapUCSC genome browser: 22q13.31
Genomic locationchr22 :44351260-44392412
Type of geneprotein-coding
RefGenesNM_015380.4,
Ensembl idENSG00000100347
Descriptionsorting and assembly machinery 50kDasorting and assembly machinery component 50 homologtransformation-related gene 3 protein
Modification date20141207
dbXrefs MIM : 612058
HGNC : HGNC
Ensembl : ENSG00000100347
HPRD : 10826
Vega : OTTHUMG00000150557
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SAMM50
BioGPS: 25813
Gene Expression Atlas: ENSG00000100347
The Human Protein Atlas: ENSG00000100347
PathwayNCI Pathway Interaction Database: SAMM50
KEGG: SAMM50
REACTOME: SAMM50
ConsensusPathDB
Pathway Commons: SAMM50
MetabolismMetaCyc: SAMM50
HUMANCyc: SAMM50
RegulationEnsembl's Regulation: ENSG00000100347
miRBase: chr22 :44,351,260-44,392,412
TargetScan: NM_015380
cisRED: ENSG00000100347
ContextiHOP: SAMM50
cancer metabolism search in PubMed: SAMM50
UCL Cancer Institute: SAMM50
Assigned class in ccmGDBC

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Phenotypic Information for SAMM50(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SAMM50
Familial Cancer Database: SAMM50
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SAMM50
MedGen: SAMM50 (Human Medical Genetics with Condition)
ClinVar: SAMM50
PhenotypeMGI: SAMM50 (International Mouse Phenotyping Consortium)
PhenomicDB: SAMM50

Mutations for SAMM50
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SAMM50 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB528606SAMM5019243224438625444392409UNC5B235667107306171673062148
BE094760DDX5623925974460943344609453SAMM50247576224436464544369153

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             1   
GAIN (# sample)             1   
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr22:44368122-44368122p.D110G2
chr22:44372632-44372632p.H260H2
chr22:44385003-44385003p.G363D2
chr22:44373840-44373840p.?1
chr22:44364687-44364687p.D104G1
chr22:44385033-44385033p.H373R1
chr22:44371952-44371952p.T222T1
chr22:44386266-44386266p.M448I1
chr22:44377294-44377294p.G320G1
chr22:44364695-44364695p.Q107*1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1114  3 1  4 1  36 4
# mutation1114  3 1  5 1  46 4
nonsynonymous SNV 1 2  3 1  5 1  14 3
synonymous SNV1 12            32 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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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
chr22:44385035p.R180L1
chr22:44360402p.G427R1
chr22:44371986p.T222T1
chr22:44385092p.I437I1
chr22:44364687p.E234K1
chr22:44371988p.V446I1
chr22:44385106p.E234D1
chr22:44368118p.M448I1
chr22:44372006p.G20G1
chr22:44386179p.R240R1

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 SAMM50 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 SAMM50

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

ACO2,ADSL,ATXN10,RTCB,SMDT1,DRG1,GCAT,
L3MBTL2,MCAT,NDUFA6,NHP2L1,PARVB,PES1,PMM1,
RANGAP1,SAMM50,ST13,TOMM22,TRMU,TXN2,XRCC6
ATP5B,ATP5G3,ATP5H,ATP5J,COX14,APOPT1,C21orf33,
CHCHD10,ECH1,FH,HADHA,MRPL46,MRPS15,NDUFA6,
NDUFA8,NDUFV3,PDHA1,GATB,SAMM50,SDHB,UQCRC2

ACO2,ADSL,ATP5F1,ATP5G3,ATXN10,CECR5,COX5A,
EIF3D,FH,LGTN,MCAT,MMACHC,MRPL35,NDUFA6,
OXSM,SAMM50,SCO2,TOMM22,TXN2,UQCRC2,XRCC6
ATP5A1,C2orf47,CLP1,CLYBL,COQ4,ECHS1,FH,
GSTK1,HADH,HSD17B8,IDH3B,IMP3,MDH2,MTCH2,
OXNAD1,ECI2,SAMM50,SDHB,SUCLG1,UQCRC2,UQCRHL
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 SAMM50


There's no related Drug.
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Cross referenced IDs for SAMM50
* 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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