Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	TOMM40
	Gene name	translocase of outer mitochondrial membrane 40 homolog (yeast)
	Synonyms	C19orf1\|D19S1177E\|PER-EC1\|PEREC1\|TOM40
	Cytomap	UCSC genome browser: 19q13
	Genomic location	chr19 :45394476-45406946
	Type of gene	protein-coding
	RefGenes	NM_001128916.1, NM_001128917.1,NM_006114.2,
	Ensembl id	ENSG00000130204
	Description	mitochondrial import receptor subunit TOM40 homologmitochondrial outer membrane proteinp38.5protein Haymakertranslocase of outer membrane 40 kDa subunit homolog
	Modification date	20141207
dbXrefs	MIM : 608061
	HGNC : HGNC
	Ensembl : ENSG00000130204
	HPRD : 16274
	Vega : OTTHUMG00000180842
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TOMM40
	BioGPS: 10452
	Gene Expression Atlas: ENSG00000130204
	The Human Protein Atlas: ENSG00000130204
Pathway	NCI Pathway Interaction Database: TOMM40
	KEGG: TOMM40
	REACTOME: TOMM40
	ConsensusPathDB
	Pathway Commons: TOMM40
Metabolism	MetaCyc: TOMM40
	HUMANCyc: TOMM40
Regulation	Ensembl's Regulation: ENSG00000130204
	miRBase: chr19 :45,394,476-45,406,946
	TargetScan: NM_001128916
	cisRED: ENSG00000130204
Context	iHOP: TOMM40
	cancer metabolism search in PubMed: TOMM40
	UCL Cancer Institute: TOMM40
Assigned class in ccmGDB	C

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Phenotypic Information for TOMM40(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: TOMM40
	MedGen: TOMM40 (Human Medical Genetics with Condition)
	ClinVar: TOMM40
Phenotype	MGI: TOMM40 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TOMM40 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BE908928	TOMM40	1	130	19	45406783	45406913	BCAP29	130	710	7	107259848	107260436
AW873110	LRTOMT	11	325	11	71808338	71808652	TOMM40	316	481	19	45404332	45406319

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr19:45397249-45397249	p.V190G	3
chr19:45404050-45404050	p.V236D	2
chr19:45404306-45404306	p.V263A	1
chr19:45395673-45395673	p.G100R	1
chr19:45404515-45404515	p.S298S	1
chr19:45395710-45395710	p.H112R	1
chr19:45404543-45404543	p.P308S	1
chr19:45396132-45396132	p.S127S	1
chr19:45406290-45406290	p.S317C	1
chr19:45397079-45397079	p.L160V	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		1			2					2	2	1			4	1	1	2
# mutation		1		1			2					2	2	1			4	1	1	2
nonsynonymous SNV												1	1				2	1		1
synonymous SNV		1		1			2					1	1	1			2		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr19:45406291	p.I323I,TOMM40	1
chr19:45395690	p.L337L,TOMM40	1
chr19:45406309	p.K349N,TOMM40	1
chr19:45396132	p.R52Q,TOMM40	1
chr19:45406351	p.I360I,TOMM40	1
chr19:45397079	p.G100R,TOMM40	1
chr19:45406387	p.V105V,TOMM40	1
chr19:45397111	p.S127S,TOMM40	1
chr19:45406420	p.L160V,TOMM40	1
chr19:45397256	p.P170P,TOMM40	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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