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 TOMM7

Basic gene info.	Gene symbol	TOMM7
	Gene name	translocase of outer mitochondrial membrane 7 homolog (yeast)
	Synonyms	TOM7
	Cytomap	UCSC genome browser: 7p15.3
	Genomic location	chr7 :22852251-22862421
	Type of gene	protein-coding
	RefGenes	NM_019059.3,
	Ensembl id	ENSG00000196683
	Description	6.2 kd proteinmitochondrial import receptor subunit TOM7 homologtranslocase of outer membrane 7 kDa subunit homolog
	Modification date	20141207
dbXrefs	MIM : 607980
	HGNC : HGNC
	Ensembl : ENSG00000196683
	HPRD : 16266
	Vega : OTTHUMG00000094805
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TOMM7
	BioGPS: 54543
	Gene Expression Atlas: ENSG00000196683
	The Human Protein Atlas: ENSG00000196683
Pathway	NCI Pathway Interaction Database: TOMM7
	KEGG: TOMM7
	REACTOME: TOMM7
	ConsensusPathDB
	Pathway Commons: TOMM7
Metabolism	MetaCyc: TOMM7
	HUMANCyc: TOMM7
Regulation	Ensembl's Regulation: ENSG00000196683
	miRBase: chr7 :22,852,251-22,862,421
	TargetScan: NM_019059
	cisRED: ENSG00000196683
Context	iHOP: TOMM7
	cancer metabolism search in PubMed: TOMM7
	UCL Cancer Institute: TOMM7
Assigned class in ccmGDB	C

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Phenotypic Information for TOMM7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TOMM7
	Familial Cancer Database: TOMM7

* 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: TOMM7
	MedGen: TOMM7 (Human Medical Genetics with Condition)
	ClinVar: TOMM7
Phenotype	MGI: TOMM7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TOMM7

Mutations for TOMM7

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	TOMM7	chr7	22852417	22852437	TOMM7	chr7	22852486	22852506
pancreas	TOMM7	chr7	22856092	22856112	TOMM7	chr7	22856022	22856042

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TOMM7 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
AW877510	NCBP1	5	119	9	100435740	100435853	TOMM7	108	183	7	22852817	22852892
AW877449	TOMM7	35	105	7	22852819	22852892	NCBP1	94	237	9	100435711	100435853
BU951526	YY1AP1	5	500	1	155629237	155629732	TOMM7	499	602	7	22862352	22862456
DW441224	TOMM7	18	262	7	22857627	22862498	SEC13	257	379	3	10342765	10342887

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

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

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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=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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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
chr7:22862334-22862334	p.A22G	1
chr7:22862367-22862367	p.R11K	1
chr7:22862386-22862386	p.S5G	1
chr7:22862394-22862394	p.V2G	1
chr7:22862303-22862303	p.I32M	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=0

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
# mutation
nonsynonymous SNV
synonymous SNV

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

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 TOMM7 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 TOMM7

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


ATP6V1A,CEP97,DCUN1D1,ESRP1,GSK3B,HLTF,KPNA1, LRRC58,MRPL3,NAA15,NAA50,NSUN3,OPA1,PCNP, QTRTD1,TRMT10C,SNX4,TBC1D23,TFG,TOMM70A,ZBTB11	ANKRD46,ARMC8,TCAIM,COPS2,IARS2,IPO5,KIAA0368, KIAA1715,KLHL24,LRPPRC,MRS2,NAA30,OPA1,PPM1A, PTCD2,RMND5A,SCRN3,SLC25A46,TOMM70A,USP25,ZFYVE9

ACTL6A,ATG3,CMSS1,CCDC58,CHCHD4,DNAJC19,EIF2A, FBXO45,GFM1,GMPS,MINA,MRPL3,MRPS22,NAA50, OPA1,QTRTD1,TRMT10C,RSRC1,TOMM70A,UBA5,UMPS	AK3___AK4,AP3M1,KANSL1L,CLCC1,CWC27,DARS,DNM1L, ENOX2,IPO11,IPO5,IPO7,KDELC2,CFAP97,LOC221710, MTAP,NUDT21,OGFOD1,PIGK,RBBP7,TOMM70A,TYW3

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 TOMM7

There's no related Drug.

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Cross referenced IDs for TOMM7

* 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