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 TOMM22
Basic gene info.Gene symbolTOMM22
Gene nametranslocase of outer mitochondrial membrane 22 homolog (yeast)
Synonyms1C9-2|MST065|MSTP065|TOM22
CytomapUCSC genome browser: 22q12-q13
Genomic locationchr22 :39077953-39080766
Type of geneprotein-coding
RefGenesNM_020243.4,
Ensembl idENSG00000100216
Descriptionmitochondrial import receptor Tom22mitochondrial import receptor subunit TOM22 homologtranslocase of outer membrane 22 kDa subunit homolog
Modification date20141207
dbXrefs MIM : 607046
HGNC : HGNC
HPRD : 06130
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TOMM22
BioGPS: 56993
Gene Expression Atlas: ENSG00000100216
The Human Protein Atlas: ENSG00000100216
PathwayNCI Pathway Interaction Database: TOMM22
KEGG: TOMM22
REACTOME: TOMM22
ConsensusPathDB
Pathway Commons: TOMM22
MetabolismMetaCyc: TOMM22
HUMANCyc: TOMM22
RegulationEnsembl's Regulation: ENSG00000100216
miRBase: chr22 :39,077,953-39,080,766
TargetScan: NM_020243
cisRED: ENSG00000100216
ContextiHOP: TOMM22
cancer metabolism search in PubMed: TOMM22
UCL Cancer Institute: TOMM22
Assigned class in ccmGDBC

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Phenotypic Information for TOMM22(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TOMM22
Familial Cancer Database: TOMM22
* 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: TOMM22
MedGen: TOMM22 (Human Medical Genetics with Condition)
ClinVar: TOMM22
PhenotypeMGI: TOMM22 (International Mouse Phenotyping Consortium)
PhenomicDB: TOMM22

Mutations for TOMM22
* 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 TOMM22 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA740171COX4I14251168584035685840606TOMM22248434223907800639078421

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr22:39078338-39078338p.T43I1
chr22:39078348-39078348p.E46D1
chr22:39078362-39078362p.L51P1
chr22:39078403-39078403p.A65T1
chr22:39078419-39078419p.S70F1
chr22:39078435-39078435p.Q75H1
chr22:39078929-39078929p.I94M1
chr22:39077991-39077991p.A3G1
chr22:39078936-39078936p.L97F1
chr22:39078053-39078053p.D24H1

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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 4       11   31 1
# mutation 1 4       11   31 1
nonsynonymous SNV 1 4       11   21 1
synonymous SNV                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
chr22:39078419p.F72C1
chr22:39078425p.Q75H1
chr22:39078435p.I94M1
chr22:39078929p.L97F1
chr22:39078936p.P98P1
chr22:39078941p.I119V1
chr22:39079772p.G122E1
chr22:39078338p.T43I1
chr22:39079782p.E46D1
chr22:39078348p.L51P1

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 TOMM22 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 TOMM22

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

ADSL,ANKRD54,ATF4,CENPM,DRG1,EIF3D,MCAT,
NDUFA6,NHP2L1,NOL12,PES1,PHF5A,POLR2F,RANBP1,
RBX1,SNRPD3,TOMM22,TRMU,TXN2,UQCR10,XRCC6
ATP5L,C14orf166,COA3,COX7A2L,CSNK2B,EIF3K,HINT1,
JAGN1,LSM3,MRPL9,NUTF2,PSMB7,PTPMT1,RPL38,
RPS20,SSBP1,SUPT4H1,TMEM223,TOMM22,TOMM6,UBA52

ADSL,BID,C14orf142,DRG1,FAM96A,GLRX3,MRPL11,
MRPS15,MRPS23,NDUFA6,NME1,NUDCD2,PHF5A,POLR2F,
PRDX3,RBX1,SF3B5,SLC25A17,TIMM8B,TOMM22,TXN2
ATP5O,DTD2,CCDC58,GLRX3,GTPBP8,MRPL11,MRPL15,
MRPL1,MRPL22,MRPL32,MRPL46,MRPS15,MRPS16,MRPS22,
MRPS7,STOML2,TAF9,TMEM183A,TMEM223,TOMM22,WDR61
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 TOMM22


There's no related Drug.
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Cross referenced IDs for TOMM22
* 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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