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 TIMM17B
Basic gene info.Gene symbolTIMM17B
Gene nametranslocase of inner mitochondrial membrane 17 homolog B (yeast)
SynonymsDXS9822|TIM17B
CytomapUCSC genome browser: Xp11.23
Genomic locationchrX :48750729-48755426
Type of geneprotein-coding
RefGenesNM_001167947.2,
NM_005834.4,
Ensembl idENSG00000267823
Descriptioninner mitochondrial membrane preprotein translocasemitochondrial import inner membrane translocase subunit Tim17-B
Modification date20141207
dbXrefs MIM : 300249
HGNC : HGNC
Ensembl : ENSG00000126768
HPRD : 02218
Vega : OTTHUMG00000034498
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TIMM17B
BioGPS: 10245
Gene Expression Atlas: ENSG00000267823
The Human Protein Atlas: ENSG00000267823
PathwayNCI Pathway Interaction Database: TIMM17B
KEGG: TIMM17B
REACTOME: TIMM17B
ConsensusPathDB
Pathway Commons: TIMM17B
MetabolismMetaCyc: TIMM17B
HUMANCyc: TIMM17B
RegulationEnsembl's Regulation: ENSG00000267823
miRBase: chrX :48,750,729-48,755,426
TargetScan: NM_001167947
cisRED: ENSG00000267823
ContextiHOP: TIMM17B
cancer metabolism search in PubMed: TIMM17B
UCL Cancer Institute: TIMM17B
Assigned class in ccmGDBC

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Phenotypic Information for TIMM17B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TIMM17B
Familial Cancer Database: TIMM17B
* 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: TIMM17B
MedGen: TIMM17B (Human Medical Genetics with Condition)
ClinVar: TIMM17B
PhenotypeMGI: TIMM17B (International Mouse Phenotyping Consortium)
PhenomicDB: TIMM17B

Mutations for TIMM17B
* 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 TIMM17B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU676136TIMM17B19332X4875073248751045SPINT1327468154114942641149567
CB250487TIMM17B19332X4875073248751045SPINT1327468154114942641149567
BM968551TIMM17B19332X4875073248751045SPINT1327467154114942641149567
BE716540PLP210242X4903111949031351TIMM17B239325X4875075648750842

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
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
chr23:48754135-48754135p.W11*2
chr23:48752352-48752352p.N53N2
chr23:48752384-48752384p.G43R1
chr23:48751296-48751296p.?1
chr23:48754088-48754088p.G27V1
chr23:48751383-48751383p.R106C1
chr23:48754099-48754099p.M23I1
chr23:48751400-48751400p.G100V1
chr23:48754113-48754113p.G19*1
chr23:48751471-48751471p.I76I1

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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
# sample1  11   1  111     3
# mutation1  11   1  111     3
nonsynonymous SNV1  1    1  111     2
synonymous SNV    1              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
chrX:48752377p.R45Q,TIMM17B1
chrX:48752378p.R45W,TIMM17B1
chrX:48752384p.G43R,TIMM17B1
chrX:48754133p.R12Q,TIMM17B1
chrX:48751096p.P145P,TIMM17B1
chrX:48751255p.G120R,TIMM17B1
chrX:48751383p.R106C,TIMM17B1
chrX:48751400p.G100V,TIMM17B1
chrX:48751501p.F66F,TIMM17B1
chrX:48751506p.S65G,TIMM17B1

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 TIMM17B 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 TIMM17B

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

ALKBH6,C1orf35,CCDC12,CCDC22,COMMD4,EBP,FAM50A,
GPKOW,HSD17B10,MAGIX,MRPL55,NDUFB11,POLR2I,PQBP1,
RBM10,RBM42,SDHAF1,TIMM17B,UXT,WDR13,WDR45
ACOT8,FAM195A,FASTK,CPTP,HSF1,MAP2K2,MRPL14,
MRPL38,NOSIP,NSUN5,PHPT1,PMF1,PMPCA,POP7,
PPP2R1A,PRMT1,PTGES2,SGTA,SIVA1,TIMM17B,TMEM134

APOO,CCDC22,EBP,EMD,FAM104B,FAM58A,FTSJ1,
FUNDC2,HSD17B10,LAGE3,MCTS1,NAA10,NDUFB11,PDZD11,
PQBP1,PRDX4,RNF113A,SSR4,SUV39H1,TIMM17B,UXT
ANAPC11,ARL6IP4,ASNA1,CHCHD2,CHCHD5,DPM3,FAM96B,
MRPL57,MRPL43,MRPS24,NDUFA7,NDUFB4,NUBP2,POP7,
PRDX2,PSMD8,PSMD9,RPS19BP1,SCNM1,SNX17,TIMM17B
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 TIMM17B


There's no related Drug.
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Cross referenced IDs for TIMM17B
* 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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