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 HCCS
Basic gene info.Gene symbolHCCS
Gene nameholocytochrome c synthase
SynonymsCCHL|MCOPS7|MLS
CytomapUCSC genome browser: Xp22.3
Genomic locationchrX :11129405-11141204
Type of geneprotein-coding
RefGenesNM_001122608.2,
NM_001171991.2,NM_005333.4,
Ensembl idENSG00000004961
Descriptioncytochrome c heme-lyasecytochrome c-type heme lyaseholocytochrome c-type synthasemicrophthalamia with linear skin defects
Modification date20141219
dbXrefs MIM : 300056
HGNC : HGNC
Ensembl : ENSG00000004961
HPRD : 02085
Vega : OTTHUMG00000021128
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HCCS
BioGPS: 3052
Gene Expression Atlas: ENSG00000004961
The Human Protein Atlas: ENSG00000004961
PathwayNCI Pathway Interaction Database: HCCS
KEGG: HCCS
REACTOME: HCCS
ConsensusPathDB
Pathway Commons: HCCS
MetabolismMetaCyc: HCCS
HUMANCyc: HCCS
RegulationEnsembl's Regulation: ENSG00000004961
miRBase: chrX :11,129,405-11,141,204
TargetScan: NM_001122608
cisRED: ENSG00000004961
ContextiHOP: HCCS
cancer metabolism search in PubMed: HCCS
UCL Cancer Institute: HCCS
Assigned class in ccmGDBC

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Phenotypic Information for HCCS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HCCS
Familial Cancer Database: HCCS
* 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
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM

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

Mutations for HCCS
* 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 HCCS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF857908HCCS25187X1113019911133036IQSEC117950131302054813020870

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

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=4)
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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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
chr23:11139095-11139095p.R197Q2
chr23:11139860-11139860p.R246H1
chr23:11132998-11132998p.K48N1
chr23:11135463-11135463p.P110L1
chr23:11139874-11139874p.S251T1
chr23:11133033-11133033p.A60V1
chr23:11135492-11135492p.Y120H1
chr23:11139875-11139875p.S251L1
chr23:11133043-11133043p.Y63Y1
chr23:11136637-11136637p.E140K1

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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
# sample21 61 1 1  2    2211
# mutation21 61 1 1  2    2211
nonsynonymous SNV2  41 1 1  1    1111
synonymous SNV 1 2       1    11  
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
chrX:11139773p.R217H,HCCS2
chrX:11133033p.M32I,HCCS1
chrX:11139095p.K48N,HCCS1
chrX:11133052p.G232V,HCCS1
chrX:11139756p.A60V,HCCS1
chrX:11133053p.R246H,HCCS1
chrX:11139765p.C66C,HCCS1
chrX:11133059p.S251T,HCCS1
chrX:11133074p.P67T,HCCS1
chrX:11139818p.R265H,HCCS1

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 HCCS 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 HCCS

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

ARSD,B4GALNT1,CCT5,CDK4,DYRK2,EPR1,FANCB,
FUCA2,GEMIN8,GJA10,HCCS,MARCH11,METTL7B,MOSPD2,
OR9K2,PIGA,PIR,SYNGR2,TK1,TRIM55,USP36
ACYP2,BTBD1,CAP2,CFL2,CISD1,COQ3,COX5A,
CUTC,CYCS,EPM2A,FEZ2,FKBP3,GRSF1,GYG1,
HCCS,KPNA3,MRPL15,MYL12A,NDUFB3,VDAC1,VDAC3

APOO,ATP6AP2,CXorf40A,ELK1,FTSJ1,HCCS,MCTS1,
MSL3,PDHA1,PDZD11,PIGA,PRDX4,PRPS2,PSMD10,
RP2,SCML1,SLC25A5,SMS,UBE2A,UXT,VBP1
ABI1,ARPC5,ATP5B,BAK1,COX5A,CXorf40A,DBI,
GHITM,HCCS,HN1,IMPA1,MAD2L1BP,MYL12A,OSTF1,
PLEKHF2,TDRD7,TMSB4XP8,TPMT,UBE2A,UBE2D2,VAMP8
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 HCCS


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