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 CP
Basic gene info.Gene symbolCP
Gene nameceruloplasmin (ferroxidase)
SynonymsCP-2
CytomapUCSC genome browser: 3q23-q25
Genomic locationchr3 :148880196-148939832
Type of geneprotein-coding
RefGenesNM_000096.3,
NR_046371.1,
Ensembl idENSG00000047457
Descriptionceruloplasmin
Modification date20141219
dbXrefs MIM : 117700
HGNC : HGNC
Ensembl : ENSG00000047457
HPRD : 00317
Vega : OTTHUMG00000159563
ProteinUniProt: P00450
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CP
BioGPS: 1356
Gene Expression Atlas: ENSG00000047457
The Human Protein Atlas: ENSG00000047457
PathwayNCI Pathway Interaction Database: CP
KEGG: CP
REACTOME: CP
ConsensusPathDB
Pathway Commons: CP
MetabolismMetaCyc: CP
HUMANCyc: CP
RegulationEnsembl's Regulation: ENSG00000047457
miRBase: chr3 :148,880,196-148,939,832
TargetScan: NM_000096
cisRED: ENSG00000047457
ContextiHOP: CP
cancer metabolism search in PubMed: CP
UCL Cancer Institute: CP
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CP in cancer cell metabolism1. Lokamani I, Looi ML, Md Ali SA, Mohd Dali AZ, Ahmad Annuar MA, et al. (2014) Gelsolin and ceruloplasmin as potential predictive biomarkers for cervical cancer by 2D-DIGE proteomics analysis. Pathol Oncol Res 20: 119-129. doi: 10.1007/s12253-013-9670-9. go to article
2. Babich PS, Skvortsov AN, Rusconi P, Tsymbalenko NV, Mutanen M, et al. (2013) Non-hepatic tumors change the activity of genes encoding copper trafficking proteins in the liver. Cancer Biol Ther 14: 614-624. doi: 10.4161/cbt.24594. pmid: 3742491. go to article

Top
Phenotypic Information for CP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CP
Familial Cancer Database: CP
* 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 117700; gene.
604290; phenotype.
Orphanet 48818; Aceruloplasminemia.
DiseaseKEGG Disease: CP
MedGen: CP (Human Medical Genetics with Condition)
ClinVar: CP
PhenotypeMGI: CP (International Mouse Phenotyping Consortium)
PhenomicDB: CP

Mutations for CP
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastCPchr3148913662148913662CPchr3148921377148921377
ovaryCPchr3148901465148901485PHF16chr234684371646843736
ovaryCPchr3148914523148914543CPchr3148921744148921764
ovaryCPchr3148925430148925450chr3149063055149063075
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG945303ATXN7143636395070663951571CP4344533148911232148911251

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=7

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=96)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr3:148927028-148927028p.E251K7
chr3:148939579-148939579p.?4
chr3:148939490-148939490p.E30D3
chr3:148927989-148927989p.S191*3
chr3:148905923-148905923p.E594K2
chr3:148919930-148919930p.R436Q2
chr3:148930350-148930350p.G94G2
chr3:148927978-148927978p.G195R2
chr3:148924112-148924112p.F351L2
chr3:148923985-148923985p.F393S2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample162145 4 22 882 1149 17
# mutation162175 4 22 882 11513 19
nonsynonymous SNV132135 4 12 731 1118 14
synonymous SNV 3 4    1  151  45 5
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
chr3:148927028p.E251K4
chr3:148927978p.G195R2
chr3:148928050p.D103D2
chr3:148897410p.G708D2
chr3:148930323p.D171N2
chr3:148903188p.S865F2
chr3:148928058p.G168V2
chr3:148897421p.L919L1
chr3:148916279p.G569W1
chr3:148928072p.P387P1

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 CP 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 CP

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

ACADM,ALDH6A1,ATPAF1,BSDC1,C1orf210,TCEANC2,CPT2,
DHCR24,IPP,IVD,KIAA0319L,MYCBP,NRD1,NSUN4,
OMA1,PAFAH2,PARS2,POMGNT1,SCP2,TMEM59,YIPF1
ABCB6,ACADM,AIFM1,MPC2,C19orf54,GUCD1,COQ6,
CPT2,CRAT,CSPG5,DBI,GRPEL1,HIST1H1C,IVD,
LDHD,NDUFA10,NDUFAF1,NFS1,PCCB,ECI2,SUOX

ABCD3,ACADS,ALDH6A1,ARHGEF16,C1orf210,CPT2,DLST,
ETFDH,GGT6,GPBP1L1,HMGCL,LDHD,NUDT6,OMA1,
PAFAH2,PIGR,RBM47,RPS6KA1,SCP2,SIAE,TMEM125
ACSF2,AGFG2,AP1M2,BDH1,CPT2,DTX4,ENTPD5,
EPB41L4B,KLF5,LDLRAP1,MARVELD3,MYO1D,PAFAH2,PLD1,
PPARG,PTK6,SFXN5,SH3BGRL2,SLC44A1,TRAF3IP2,WDR78
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 CP
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA26815; -.
Organism-specific databasesCTD 1356; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033ceruloplasmin (ferroxidase)approvedMercaptopurine
DB00563ceruloplasmin (ferroxidase)approvedMethotrexate


Top
Cross referenced IDs for CP
* 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