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 CYC1
Basic gene info.Gene symbolCYC1
Gene namecytochrome c-1
SynonymsMC3DN6|UQCR4
CytomapUCSC genome browser: 8q24.3
Genomic locationchr8 :145149959-145152428
Type of geneprotein-coding
RefGenesNM_001916.4,
Ensembl idENSG00000179091
Descriptioncomplex III subunit 4complex III subunit IVcytochrome b-c1 complex subunit 4cytochrome c1, heme protein, mitochondrialubiquinol-cytochrome-c reductase complex cytochrome c1 subunit
Modification date20141207
dbXrefs MIM : 123980
HGNC : HGNC
Ensembl : ENSG00000179091
HPRD : 00480
Vega : OTTHUMG00000165242
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CYC1
BioGPS: 1537
Gene Expression Atlas: ENSG00000179091
The Human Protein Atlas: ENSG00000179091
PathwayNCI Pathway Interaction Database: CYC1
KEGG: CYC1
REACTOME: CYC1
ConsensusPathDB
Pathway Commons: CYC1
MetabolismMetaCyc: CYC1
HUMANCyc: CYC1
RegulationEnsembl's Regulation: ENSG00000179091
miRBase: chr8 :145,149,959-145,152,428
TargetScan: NM_001916
cisRED: ENSG00000179091
ContextiHOP: CYC1
cancer metabolism search in PubMed: CYC1
UCL Cancer Institute: CYC1
Assigned class in ccmGDBC

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Phenotypic Information for CYC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CYC1
MedGen: CYC1 (Human Medical Genetics with Condition)
ClinVar: CYC1
PhenotypeMGI: CYC1 (International Mouse Phenotyping Consortium)
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.

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 CYC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI006405CYC1221358145151165145151280C1QB13221312298743422987515
BM562582MIS18A1624213364203033651341CYC16259068145151031145151395
BM423739MIS18A26649213364203033651341CYC16508668145151031145151331
BC033076MIS18A1624213364203033651341CYC162514618145151031145152428
BC011661CYC1508198145151098145152428TRBV20-181917481620120622014815

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample   1             
GAIN (# sample)   1             
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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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=4

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check002.gifSomatic 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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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
chr8:145150101-145150101p.R33R4
chr8:145151572-145151572p.F233I2
chr8:145150876-145150876p.S93fs*1612
chr8:145151587-145151587p.P238S2
chr8:145151387-145151387p.V201M2
chr8:145151520-145151520p.L215L2
chr8:145152017-145152017p.R285*2
chr8:145150875-145150876p.S93fs*261
chr8:145151106-145151106p.V136M1
chr8:145152211-145152211p.R317P1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  31 2 1  341 13313
# mutation2  31 2 1  351 13313
nonsynonymous SNV1  11      241  3113
synonymous SNV1  2  2 1  11  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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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
chr8:145150852p.V82V2
chr8:145151587p.P238S2
chr8:145151348p.Y218F1
chr8:145151615p.A72A1
chr8:145150822p.P222A1
chr8:145151387p.L78V1
chr8:145151959p.T223T1
chr8:145150838p.F233I1
chr8:145151394p.D86N1
chr8:145152190p.F129F1

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 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

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

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
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 CYC1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB04141cytochrome c-1experimental2-Hexyloxy-6-Hydroxymethyl-Tetrahydro-Pyran-3,4,5-Triol
DB04799cytochrome c-1experimental5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole
DB07401cytochrome c-1experimentalMETHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE
DB07636cytochrome c-1experimental5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE
DB07763cytochrome c-1experimental(5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE
DB07778cytochrome c-1experimentalFAMOXADONE
DB08330cytochrome c-1experimentalMETHYL (2Z)-3-METHOXY-2-{2-[(E)-2-PHENYLVINYL]PHENYL}ACRYLATE
DB08453cytochrome c-1experimental2-NONYL-4-HYDROXYQUINOLINE N-OXIDE
DB08690cytochrome c-1experimentalUBIQUINONE-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



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