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 CLPS
Basic gene info.Gene symbolCLPS
Gene namecolipase, pancreatic
Synonyms-
CytomapUCSC genome browser: 6p21.31
Genomic locationchr6 :35762758-35765121
Type of geneprotein-coding
RefGenesNM_001252597.1,
NM_001252598.1,NM_001832.3,
Ensembl idENSG00000137392
Descriptioncolipasepancreatic colipase preproprotein
Modification date20141207
dbXrefs MIM : 120105
HGNC : HGNC
Ensembl : ENSG00000137392
HPRD : 00356
Vega : OTTHUMG00000014578
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CLPS
BioGPS: 1208
Gene Expression Atlas: ENSG00000137392
The Human Protein Atlas: ENSG00000137392
PathwayNCI Pathway Interaction Database: CLPS
KEGG: CLPS
REACTOME: CLPS
ConsensusPathDB
Pathway Commons: CLPS
MetabolismMetaCyc: CLPS
HUMANCyc: CLPS
RegulationEnsembl's Regulation: ENSG00000137392
miRBase: chr6 :35,762,758-35,765,121
TargetScan: NM_001252597
cisRED: ENSG00000137392
ContextiHOP: CLPS
cancer metabolism search in PubMed: CLPS
UCL Cancer Institute: CLPS
Assigned class in ccmGDBC

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

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

Mutations for CLPS
* 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 CLPS 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=11)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr6:35762976-35762976p.I96V2
chr6:35765001-35765001p.R22P2
chr6:35765035-35765035p.A11T2
chr6:35763027-35763027p.P79S2
chr6:35762936-35762936p.R109H2
chr6:35762943-35762943p.A107T2
chr6:35764997-35764997p.G23G2
chr6:35762985-35762985p.V93M1
chr6:35765004-35765004p.P21L1
chr6:35762990-35762990p.T91I1

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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
# sample   3     1 31   92  
# mutation   2     1 31   82  
nonsynonymous SNV   2     1 1    62  
synonymous SNV           21   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
chr6:35762936p.G23G,CLPS2
chr6:35765035p.A11T,CLPS2
chr6:35764997p.R68H,CLPS2
chr6:35765000p.T50I,CLPS1
chr6:35765001p.G47R,CLPS1
chr6:35765004p.R41C,CLPS1
chr6:35765005p.S61S,CLPS1
chr6:35762985p.E29K,CLPS1
chr6:35765033p.R22R,CLPS1
chr6:35762990p.R22P,CLPS1

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 CLPS 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 CLPS

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

CELA3A,CELA3B,CLPS,CPA1,CTRB1,CTRB2,CTRC,
EFCAB10,GRK1,GRXCR1,LOC339788,LOXHD1,NOBOX,NT5C1B,
POM121L8P,POU5F1B,REG3A,SYCN,TPD52L3,TSGA10IP,ZAR1L
VRTN,C1QTNF8,C7orf33,CHD5,CLPS,COL9A1,CPNE6,
DRP2,HBG1,HBG2,ITIH3,ITLN1,KIF1A,MLC1,
NKX2-3,NOBOX,P2RX1,POU5F1B,SOST,WFDC1,ZFP42

AMY2A,C11orf40,BPIFB3,NAT16,CELA2A,CELA2B,CELA3A,
CELA3B,CLPS,CPA1,CPB1,CTRB1,CTRB2,CTRC,
DEFB109P1,OPRM1,OR6X1,PCDH19,PLA2G1B,PNLIP,SYCN
ANKRD30B,CYP4F30P,SPTSSB,CLPS,CREB3L4,GPR98,HAPLN1,
HMGN1,HPVC1,IGFALS,LOC100128023,LOC284578,LRRC36,LYPD6,
MFSD6L,PARP8,PAX4,RLN2,TMEFF2,TMEM231,WFDC2
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 CLPS
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
DB04233colipase, pancreaticexperimental(Hydroxyethyloxy)Tri(Ethyloxy)Octane
DB08222colipase, pancreaticexperimentalMETHOXYUNDECYLPHOSPHINIC ACID


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Cross referenced IDs for CLPS
* 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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