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 TOMM40
Basic gene info.Gene symbolTOMM40
Gene nametranslocase of outer mitochondrial membrane 40 homolog (yeast)
SynonymsC19orf1|D19S1177E|PER-EC1|PEREC1|TOM40
CytomapUCSC genome browser: 19q13
Genomic locationchr19 :45394476-45406946
Type of geneprotein-coding
RefGenesNM_001128916.1,
NM_001128917.1,NM_006114.2,
Ensembl idENSG00000130204
Descriptionmitochondrial import receptor subunit TOM40 homologmitochondrial outer membrane proteinp38.5protein Haymakertranslocase of outer membrane 40 kDa subunit homolog
Modification date20141207
dbXrefs MIM : 608061
HGNC : HGNC
Ensembl : ENSG00000130204
HPRD : 16274
Vega : OTTHUMG00000180842
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TOMM40
BioGPS: 10452
Gene Expression Atlas: ENSG00000130204
The Human Protein Atlas: ENSG00000130204
PathwayNCI Pathway Interaction Database: TOMM40
KEGG: TOMM40
REACTOME: TOMM40
ConsensusPathDB
Pathway Commons: TOMM40
MetabolismMetaCyc: TOMM40
HUMANCyc: TOMM40
RegulationEnsembl's Regulation: ENSG00000130204
miRBase: chr19 :45,394,476-45,406,946
TargetScan: NM_001128916
cisRED: ENSG00000130204
ContextiHOP: TOMM40
cancer metabolism search in PubMed: TOMM40
UCL Cancer Institute: TOMM40
Assigned class in ccmGDBC

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Phenotypic Information for TOMM40(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TOMM40
Familial Cancer Database: TOMM40
* 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: TOMM40
MedGen: TOMM40 (Human Medical Genetics with Condition)
ClinVar: TOMM40
PhenotypeMGI: TOMM40 (International Mouse Phenotyping Consortium)
PhenomicDB: TOMM40

Mutations for TOMM40
* 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 TOMM40 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE908928TOMM401130194540678345406913BCAP291307107107259848107260436
AW873110LRTOMT11325117180833871808652TOMM40316481194540433245406319

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 # sample1                
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr19:45397249-45397249p.V190G3
chr19:45404050-45404050p.V236D2
chr19:45396132-45396132p.S127S1
chr19:45406290-45406290p.S317C1
chr19:45397079-45397079p.L160V1
chr19:45406291-45406291p.S317S1
chr19:45397111-45397111p.P170P1
chr19:45406309-45406309p.I323I1
chr19:45406387-45406387p.K349N1
chr19:45397256-45397256p.G192G1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 1  2    221  4112
# mutation 1 1  2    221  4112
nonsynonymous SNV           11   21 1
synonymous SNV 1 1  2    111  2 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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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
chr19:45397079p.G192G,TOMM401
chr19:45406387p.T226T,TOMM401
chr19:45397111p.L229L,TOMM401
chr19:45406420p.R239W,TOMM401
chr19:45397256p.S298S,TOMM401
chr19:45404021p.S317C,TOMM401
chr19:45404028p.S317S,TOMM401
chr19:45404058p.I323I,TOMM401
chr19:45404515p.L337L,TOMM401
chr19:45394827p.K349N,TOMM401

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 TOMM40 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 TOMM40

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

ATAD3A,BCL2L12,DAZAP1,DDX49,ECE2,EIF5A,EXOSC5,
GEMIN7,MRPL12,MYPOP,NOP16,POLR2F,PPAN,PRMT1,
PUS1,RPS19,RRP1,SNRPA,SNRPD2,TOMM40,UBE2S
ASPSCR1,ATAD3A,CTU2,DAZAP1,DDX54,FARSA,HDGFRP2,
LRWD1,MPND,NOC2L,NUBP2,PES1,PNKP,PRPF31,
RRP1,RRP9,RUVBL2,TIMM13,TMED1,TOMM40,ZNF787

BCL2L12,BOLA3,CCDC86,HSPBP1,MRPL12,MRPL4,PA2G4,
POLD1,PRPF31,PUS1,RANBP1,RUVBL2,SLC25A10,SLC25A39,
SNRPA,SNRPF,SRM,TCOF1,ALYREF,TIMM44,TOMM40
ATAD3A,BYSL,CCDC86,DPH2,FARSA,GRWD1,NOP14,
NOP2,PDF,PPAN,PPIF,PUS1,PYCRL,RRP1,
RRP9,SRSF2,SLC25A19,ALYREF,TOMM40,WDR4,ZMYND19
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 TOMM40


There's no related Drug.
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Cross referenced IDs for TOMM40
* 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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