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 PROC
Basic gene info.Gene symbolPROC
Gene nameprotein C (inactivator of coagulation factors Va and VIIIa)
SynonymsAPC|PC|PROC1|THPH3|THPH4
CytomapUCSC genome browser: 2q13-q14
Genomic locationchr2 :128175995-128186822
Type of geneprotein-coding
RefGenesNM_000312.3,
Ensembl idENSG00000115718
Descriptionanticoagulant protein Cautoprothrombin IIAblood coagulation factor XIVprepro-protein Cvitamin K-dependent protein C
Modification date20141207
dbXrefs MIM : 612283
HGNC : HGNC
Ensembl : ENSG00000115718
HPRD : 01466
Vega : OTTHUMG00000131528
ProteinUniProt: P04070
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PROC
BioGPS: 5624
Gene Expression Atlas: ENSG00000115718
The Human Protein Atlas: ENSG00000115718
PathwayNCI Pathway Interaction Database: PROC
KEGG: PROC
REACTOME: PROC
ConsensusPathDB
Pathway Commons: PROC
MetabolismMetaCyc: PROC
HUMANCyc: PROC
RegulationEnsembl's Regulation: ENSG00000115718
miRBase: chr2 :128,175,995-128,186,822
TargetScan: NM_000312
cisRED: ENSG00000115718
ContextiHOP: PROC
cancer metabolism search in PubMed: PROC
UCL Cancer Institute: PROC
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PROC(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PROC
Familial Cancer Database: PROC
* 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 176860; phenotype.
612283; gene.
612304; phenotype.
Orphanet 745; Hereditary thrombophilia due to congenital protein C deficiency.
DiseaseKEGG Disease: PROC
MedGen: PROC (Human Medical Genetics with Condition)
ClinVar: PROC
PhenotypeMGI: PROC (International Mouse Phenotyping Consortium)
PhenomicDB: PROC

Mutations for PROC
* 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 PROC 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

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr2:128185950-128185950p.R272C3
chr2:128178901-128178901p.R38Q2
chr2:128180872-128180872p.S141S2
chr2:128185973-128185973p.D279D2
chr2:128178999-128178999p.E71K2
chr2:128186241-128186241p.P369S2
chr2:128186037-128186037p.A301T2
chr2:128184716-128184716p.C238C2
chr2:128186044-128186044p.L303R2
chr2:128178882-128178882p.R32S1

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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
# sample11 31 1 4  4 1  9326
# mutation11 31 1 4  6 1  12327
nonsynonymous SNV 1 3    4    1  9214
synonymous SNV1   1 1    6    3113
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
chr2:128186037p.A301T2
chr2:128186044p.L303R2
chr2:128178999p.Q207Q1
chr2:128186455p.H345Q1
chr2:128185973p.R219R1
chr2:128186211p.R354K1
chr2:128180683p.K233N1
chr2:128186496p.V359I1
chr2:128185988p.C238C1
chr2:128186234p.P366P1

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 PROC 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 PROC

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

APCS,APOA4,APOC4,ASGR2,SLC25A47,C8A,C8G,
CATSPER1,CRP,F2,F9,G6PC,HAMP,HP,
ITIH1,ITIH4,LEAP2,MT1B,PLG,PROC,SERPINC1
A1CF,ANKFN1,ANKRD30B,SMCO3,C8B,CSAG2,FGL1,
HABP2,HNF1A,IGFL2,KCNC2,LOC285733,LOC646813,MIA2,
OR52M1,PKHD1,PROC,SERPINA4,TMED6,TTLL6,UGT2B15

CNPPD1,C2orf68,MLLT4-AS1,CCDC115,DDX19B,DHRS12,DNAJB2,
DNMT3A,FCHSD1,GGT7,GLB1L,IFT172,IHH,ILDR1,
MAGED2,NCK2,PROC,TMEM150A,TMEM176A,TMEM44,WBP1
AKAP5,ARHGAP36,CCDC24,CTSE,FCHSD1,HEPACAM2,IP6K2,
MCF2L,PP14571,PROC,QPRT,REP15,RORC,TCP10,
TMEM98,VSIG2,ZBTB48,ZNF552,ZNF613,ZNF763,ZNF774
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 PROC
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04070; -.
ChemistryChEMBL CHEMBL4444; -.
Organism-specific databasesPharmGKB PA33799; -.
Organism-specific databasesCTD 5624; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00170protein C (inactivator of coagulation factors Va and VIIIa)approved; nutraceuticalMenadione
DB00464protein C (inactivator of coagulation factors Va and VIIIa)approvedSodium Tetradecyl Sulfate
DB00682protein C (inactivator of coagulation factors Va and VIIIa)approvedWarfarin


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Cross referenced IDs for PROC
* 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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