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 TOMM20

Basic gene info.	Gene symbol	TOMM20
	Gene name	translocase of outer mitochondrial membrane 20 homolog (yeast)
	Synonyms	MAS20\|MOM19\|TOM20
	Cytomap	UCSC genome browser: 1q42
	Genomic location	chr1 :235272657-235292256
	Type of gene	protein-coding
	RefGenes	NM_014765.2,
	Ensembl id	ENSG00000173726
	Description	mitochondrial 20 kDa outer membrane proteinmitochondrial import receptor subunit TOM20 homologouter mitochondrial membrane receptor Tom20translocase of outer mitochondrial membrane 20 homolog type II
	Modification date	20141207
dbXrefs	MIM : 601848
	HGNC : HGNC
	Ensembl : ENSG00000173726
	HPRD : 03507
	Vega : OTTHUMG00000039619
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TOMM20
	BioGPS: 9804
	Gene Expression Atlas: ENSG00000173726
	The Human Protein Atlas: ENSG00000173726
Pathway	NCI Pathway Interaction Database: TOMM20
	KEGG: TOMM20
	REACTOME: TOMM20
	ConsensusPathDB
	Pathway Commons: TOMM20
Metabolism	MetaCyc: TOMM20
	HUMANCyc: TOMM20
Regulation	Ensembl's Regulation: ENSG00000173726
	miRBase: chr1 :235,272,657-235,292,256
	TargetScan: NM_014765
	cisRED: ENSG00000173726
Context	iHOP: TOMM20
	cancer metabolism search in PubMed: TOMM20
	UCL Cancer Institute: TOMM20
Assigned class in ccmGDB	C

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Phenotypic Information for TOMM20(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TOMM20
	Familial Cancer Database: TOMM20

* 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: TOMM20
	MedGen: TOMM20 (Human Medical Genetics with Condition)
	ClinVar: TOMM20
Phenotype	MGI: TOMM20 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TOMM20

Mutations for TOMM20

* 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 TOMM20 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
BI561585	SLC20A1	11	83	2	113403596	113403668	TOMM20	74	783	1	235275145	235292066
BF809919	TOMM20	5	147	1	235273945	235274086	SARNP	146	214	12	56194347	56194415

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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=4)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr1:235277211-235277211	p.G89S	1
chr1:235283152-235283152	p.G77G	1
chr1:235283208-235283208	p.D59N	1
chr1:235291927-235291927	p.K35R	1
chr1:235291954-235291954	p.R26H	1
chr1:235291986-235291986	p.A15A	1
chr1:235292003-235292003	p.A10T	1
chr1:235275430-235275431	p.?	1
chr1:235292007-235292007	p.I8I	1
chr1:235277103-235277103	p.K125*	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	2				1							1	1	1
# mutation	2				1							1	1	1
nonsynonymous SNV	1				1									1
synonymous SNV	1											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
chr1:235291986	p.V90V	1
chr1:235292007	p.G89S	1
chr1:235277206	p.D59N	1
chr1:235277211	p.R26H	1
chr1:235283208	p.A15A	1
chr1:235291954	p.I8I	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 TOMM20 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 TOMM20

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


ABCB10,AHCTF1,ARID4B,B3GALNT2,DIEXF,FBXO28,GGPS1, GNPAT,HEATR1,HNRNPU,IRF2BP2,NUP133,RAB4A,RBM34, RRP15,TAF5L,TARBP1,TBCE,TFB2M,TOMM20,TSNAX	CCNB1IP1,EIF2A,EIF2S3,EIF3E,EIF3L,ELF5,METTL21B, KHDRBS1,KIT,METAP1,PABPC1,PDCD4,RBMX,RSL1D1, RSL24D1,SH3YL1,TIGD2,TMEM87A,TOMM20,ZCCHC7,ZNF277

ACBD6,ADSS,C1orf43,CD46,COG2,DAP3,MRPL9, NUP133,POLR3C,PRUNE,RAB4A,RBM34,RRP15,SNRPE, SPHAR,TBCE,TFB2M,TIPRL,TOMM20,TSNAX,UFC1	C11orf1,ZFAS1,CCNB1IP1,CLNS1A,EEF1A1,EEF1A1P9,EIF2A, EIF3E,EIF3H,GAS5,NACA,RPL10,RPL10A,RPL14, RPL15,RPL32,RPL3,RPL5,RSL1D1,TATDN1,TOMM20

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 TOMM20

There's no related Drug.

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Cross referenced IDs for TOMM20

* 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