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 CYC1

Basic gene info.	Gene symbol	CYC1
	Gene name	cytochrome c-1
	Synonyms	MC3DN6\|UQCR4
	Cytomap	UCSC genome browser: 8q24.3
	Genomic location	chr8 :145149959-145152428
	Type of gene	protein-coding
	RefGenes	NM_001916.4,
	Ensembl id	ENSG00000179091
	Description	complex III subunit 4complex III subunit IVcytochrome b-c1 complex subunit 4cytochrome c1, heme protein, mitochondrialubiquinol-cytochrome-c reductase complex cytochrome c1 subunit
	Modification date	20141207
dbXrefs	MIM : 123980
	HGNC : HGNC
	Ensembl : ENSG00000179091
	HPRD : 00480
	Vega : OTTHUMG00000165242
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CYC1
	BioGPS: 1537
	Gene Expression Atlas: ENSG00000179091
	The Human Protein Atlas: ENSG00000179091
Pathway	NCI Pathway Interaction Database: CYC1
	KEGG: CYC1
	REACTOME: CYC1
	ConsensusPathDB
	Pathway Commons: CYC1
Metabolism	MetaCyc: CYC1
	HUMANCyc: CYC1
Regulation	Ensembl's Regulation: ENSG00000179091
	miRBase: chr8 :145,149,959-145,152,428
	TargetScan: NM_001916
	cisRED: ENSG00000179091
Context	iHOP: CYC1
	cancer metabolism search in PubMed: CYC1
	UCL Cancer Institute: CYC1
Assigned class in ccmGDB	C

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Phenotypic Information for CYC1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CYC1
	Familial Cancer Database: CYC1

* 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: CYC1
	MedGen: CYC1 (Human Medical Genetics with Condition)
	ClinVar: CYC1
Phenotype	MGI: CYC1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CYC1

Mutations for CYC1

* 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 CYC1 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
BI006405	CYC1	22	135	8	145151165	145151280	C1QB	132	213	1	22987434	22987515
BM562582	MIS18A	1	624	21	33642030	33651341	CYC1	625	906	8	145151031	145151395
BM423739	MIS18A	26	649	21	33642030	33651341	CYC1	650	866	8	145151031	145151331
BC033076	MIS18A	1	624	21	33642030	33651341	CYC1	625	1461	8	145151031	145152428
BC011661	CYC1	50	819	8	145151098	145152428	TRBV20-1	819	1748	16	2012062	2014815

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

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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
chr8:145150101-145150101	p.R33R	4
chr8:145151387-145151387	p.V201M	2
chr8:145151520-145151520	p.L215L	2
chr8:145152017-145152017	p.R285*	2
chr8:145151572-145151572	p.F233I	2
chr8:145150876-145150876	p.S93fs*161	2
chr8:145151587-145151587	p.P238S	2
chr8:145150758-145150758	p.S51C	1
chr8:145150889-145150889	p.P95A	1
chr8:145151615-145151615	p.P247L	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=2

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			3	1		2		1			3	4	1		1	3	3	1	3
# mutation	2			3	1		2		1			3	5	1		1	3	3	1	3
nonsynonymous SNV	1			1	1							2	4	1			3	1	1	3
synonymous SNV	1			2			2		1			1	1			1		2

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
chr8:145150852	p.V82V	2
chr8:145151587	p.P238S	2
chr8:145151504	p.L78V	1
chr8:145152203	p.T223T	1
chr8:145150862	p.F233I	1
chr8:145151520	p.D86N	1
chr8:145152211	p.F129F	1
chr8:145151087	p.P247A	1
chr8:145151528	p.L135L	1
chr8:145152212	p.P247L	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 CYC1 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 CYC1

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


BOP1,HGH1,COMMD5,CYC1,CYHR1,DGAT1,EXOSC4, FBXL6,GPAA1,SLC52A2,HSF1,MAF1,C8orf82,PUF60, PYCRL,RECQL4,RPL8,SHARPIN,TIGD5,TOP1MT,VPS28	ACO2,ATP5A1,ATP5B,ADCK3,COQ9,COX5A,CYC1, GYS1,MDH2,MRPS7,NDUFB10,NDUFB9,NDUFS2,NDUFS7, POLDIP2,RAD23A,SDHA,SIRT2,SLC25A11,TRPT1,UQCRC1

HGH1,NDUFAF6,C8orf76,COMMD5,COPS5,CYC1,EEF1D, EXOSC4,GPAA1,MAF1,MRPL11,MRPL13,MRPL15,MRPS28, NDUFB9,NSMCE2,PUF60,PYCRL,RPL8,TCEB1,TMEM70	ABT1,ATP5O,C19orf70,PRADC1,CYC1,DCTPP1,MRPL11, MRPL15,MRPL27,MRPS12,MRPS7,NDUFS3,SF3B5,SLC25A11, STOML2,PAM16,TMEM183A,TMEM223,TOMM22,TRUB2,TXN2

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 CYC1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB04141	cytochrome c-1	experimental	2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB04799	cytochrome c-1	experimental	5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole
DB07401	cytochrome c-1	experimental	METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE
DB07636	cytochrome c-1	experimental	5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE
DB07763	cytochrome c-1	experimental	(5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE
DB07778	cytochrome c-1	experimental	FAMOXADONE
DB08330	cytochrome c-1	experimental	METHYL (2Z)-3-METHOXY-2-{2-[(E)-2-PHENYLVINYL]PHENYL}ACRYLATE
DB08453	cytochrome c-1	experimental	2-NONYL-4-HYDROXYQUINOLINE N-OXIDE
DB08690	cytochrome c-1	experimental	UBIQUINONE-2

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Cross referenced IDs for CYC1

* 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