Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 SCO2
Basic gene info.Gene symbolSCO2
Gene nameSCO2 cytochrome c oxidase assembly protein
SynonymsCEMCOX1|MYP6|SCO1L
CytomapUCSC genome browser: 22q13.33
Genomic locationchr22 :50961996-50964868
Type of geneprotein-coding
RefGenesNM_001169109.1,
NM_001169110.1,NM_001169111.1,NM_005138.2,
Ensembl idENSG00000130489
DescriptionSCO cytochrome oxidase deficient homolog 2protein SCO2 homolog, mitochondrial
Modification date20141207
dbXrefs MIM : 604272
HGNC : HGNC
Ensembl : ENSG00000130489
HPRD : 05042
Vega : OTTHUMG00000150251
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SCO2
BioGPS: 9997
Gene Expression Atlas: ENSG00000130489
The Human Protein Atlas: ENSG00000130489
PathwayNCI Pathway Interaction Database: SCO2
KEGG: SCO2
REACTOME: SCO2
ConsensusPathDB
Pathway Commons: SCO2
MetabolismMetaCyc: SCO2
HUMANCyc: SCO2
RegulationEnsembl's Regulation: ENSG00000130489
miRBase: chr22 :50,961,996-50,964,868
TargetScan: NM_001169109
cisRED: ENSG00000130489
ContextiHOP: SCO2
cancer metabolism search in PubMed: SCO2
UCL Cancer Institute: SCO2
Assigned class in ccmGDBC

Top
Phenotypic Information for SCO2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SCO2
Familial Cancer Database: SCO2
* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SCO2
MedGen: SCO2 (Human Medical Genetics with Condition)
ClinVar: SCO2
PhenotypeMGI: SCO2 (International Mouse Phenotyping Consortium)
PhenomicDB: SCO2

Mutations for SCO2
* 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 SCO2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=22)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr22:50962782-50962782p.R20P4
chr22:50962330-50962330p.R171W2
chr22:50962178-50962178p.I221I2
chr22:50962183-50962183p.Y220H2
chr22:50962224-50962224p.R206H2
chr22:50962057-50962057p.R262C1
chr22:50962076-50962076p.R255R1
chr22:50962398-50962398p.V148G1
chr22:50962077-50962077p.R255Q1
chr22:50962405-50962405p.Q146*1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1 1  3  1 2     1 2
# mutation 1 1  7  1 2     1 2
nonsynonymous SNV   1  5  1 2       1
synonymous SNV 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])

Top
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
chr22:50962076p.R255R,SCO21
chr22:50962761p.D234N,SCO21
chr22:50962141p.H224R,SCO21
chr22:50962769p.I221I,SCO21
chr22:50962170p.Y180Y,SCO21
chr22:50962803p.V174I,SCO21
chr22:50962178p.R112R,SCO21
chr22:50962824p.E83D,SCO21
chr22:50962301p.E81K,SCO21
chr22:50962321p.E45K,SCO21

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 SCO2 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]

Top
Gene Expression for SCO2

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ALG12,ARSA,CHKB,CRELD2,GUK1,LMF2,NCAPH2,
NOL12,ODF3B,PRR5,RPS19BP1,PPP6R2,SCO2,SELO,
THAP7,TMUB1,TOM1,TRABD,TRMU,TSPO,TYMP
BAD,C19orf24,C9orf16,CFL1,COPE,DTYMK,MVB12A,
FIBP,GNB2,MPG,PPP1CA,PPP4C,PTRH1,SCO2,
SNAPC2,TBCB,TMEM208,TRAPPC5,YIF1A,YIF1B,ZDHHC12

AKR1A1,PTRHD1,ECI1,EIF5A,EIF5AL1,NAA38,MCAT,
MIF,MRPL27,MRPL43,MRPL54,NDUFA6,PSMA6,RBX1,
RPS19BP1,SCO2,SF3B5,TOMM22,TSPO,TXN2,UQCRC1
BOLA2,UQCC3,MIEN1,CCDC12,CHCHD1,DCTPP1,LOC729991,
LSM4,LSM7,MRPL14,MRPL27,MRPL54,NDUFS3,OVCA2,
PPP4C,ROMO1,SCO2,SF3B5,TMSB10,TSPO,UQCR10
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for SCO2


There's no related Drug.
Top
Cross referenced IDs for SCO2
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas