Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 PRELP

Basic gene info.	Gene symbol	PRELP
	Gene name	proline/arginine-rich end leucine-rich repeat protein
	Synonyms	MST161\|MSTP161\|SLRR2A
	Cytomap	UCSC genome browser: 1q32
	Genomic location	chr1 :203444882-203460479
	Type of gene	protein-coding
	RefGenes	NM_002725.3, NM_201348.1,
	Ensembl id	ENSG00000188783
	Description	55 kDa leucine-rich repeat protein of articular cartilageprolarginprolargin proteoglycanproline-arginine-rich end leucine-rich repeat protein
	Modification date	20141207
dbXrefs	MIM : 601914
	HGNC : HGNC
	Ensembl : ENSG00000188783
	HPRD : 03556
	Vega : OTTHUMG00000035911
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRELP
	BioGPS: 5549
	Gene Expression Atlas: ENSG00000188783
	The Human Protein Atlas: ENSG00000188783
Pathway	NCI Pathway Interaction Database: PRELP
	KEGG: PRELP
	REACTOME: PRELP
	ConsensusPathDB
	Pathway Commons: PRELP
Metabolism	MetaCyc: PRELP
	HUMANCyc: PRELP
Regulation	Ensembl's Regulation: ENSG00000188783
	miRBase: chr1 :203,444,882-203,460,479
	TargetScan: NM_002725
	cisRED: ENSG00000188783
Context	iHOP: PRELP
	cancer metabolism search in PubMed: PRELP
	UCL Cancer Institute: PRELP
Assigned class in ccmGDB	C

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Phenotypic Information for PRELP(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRELP
	Familial Cancer Database: PRELP

* 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: PRELP
	MedGen: PRELP (Human Medical Genetics with Condition)
	ClinVar: PRELP
Phenotype	MGI: PRELP (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRELP

Mutations for PRELP

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PRELP related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BU727928	CCDC36	1	321	3	49282867	49283627	PRELP	313	475	1	203452298	203452459
BQ183043	PRELP	14	573	1	203453183	203456291	LOC100507412	571	671	?	110051	110152
BM686368	PRELP	8	307	1	203444931	203452459	CCDC36	299	567	3	49282867	49283136
DA313778	LIPA	1	135	10	90977996	90978130	PRELP	128	525	1	203458346	203458743
BF986263	CHD4	9	132	12	6709750	6710130	PRELP	125	271	1	203452442	203452588

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=23)

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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Top 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 position	Mutation(aa)	Unique sampleID count
chr1:203453021-203453021	p.P237S	4
chr1:203453266-203453266	p.L318L	2
chr1:203452913-203452913	p.D201Y	2
chr1:203452395-203452395	p.P28H	2
chr1:203455833-203455833	p.?	2
chr1:203452538-203452538	p.E76K	2
chr1:203455842-203455842	p.G328R	2
chr1:203453245-203453245	p.N311K	2
chr1:203455873-203455873	p.A338V	2
chr1:203452475-203452475	p.P55S	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	2	1	11			3		2	1	1	12	5	3			3	3		10
# mutation	1	2	1	10			3		2	1	1	11	5	3			3	3		10
nonsynonymous SNV		1	1	5			3		1	1		7	3	2			2	2		7
synonymous SNV	1	1		5					1		1	4	2	1			1	1		3

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr1:203452913	p.R356Q,PRELP	2
chr1:203453266	p.R356R,PRELP	2
chr1:203455927	p.L318L,PRELP	2
chr1:203455928	p.D201Y,PRELP	2
chr1:203452615	p.R24T,PRELP	1
chr1:203455862	p.P150P,PRELP	1
chr1:203452873	p.R302M,PRELP	1
chr1:203452383	p.P28H,PRELP	1
chr1:203453217	p.A168V,PRELP	1
chr1:203452708	p.V306V,PRELP	1

Other 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

Copy Number for PRELP 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 PRELP

Gene 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.

Differential 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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CNV 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

Co-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


ACAN,BGN,NPR3,ENPEP,EXT2,FOLR1,FRZB, FXYD4,MIA,NOS2,NPR2,PANX3,PHOSPHO1,PRELP, PRSS54,S100A1,SCRG1,SLC6A18,SNAI2,TTYH1,WWP2	ABCA8,ALDH2,ANTXR2,LINC00341,C1QTNF1,CDKN2B,CRTAP, DUSP22,EBF3,FYN,GABARAPL1,GALNT15,GSN,KANK2, NDRG1,PCOLCE2,PRELP,SLC9A9,TBC1D2B,TMBIM1,VIM

AOC3,BOC,CDO1,CPXM2,EFEMP1,FBLN5,FHL1, GPIHBP1,LHFP,MGP,PODN,PRELP,PTGIS,PTH1R, RBMS3,RNF180,SLIT2,SLIT3,STON1,TCF7L1,TMEM130	ADAMTSL3,BOC,CC2D2A,CD81,CLIP3,DIP2C,FGFR1, GLI3,GPRASP1,GRIK5,MID2,NPR2,PDE2A,PEG3, PRELP,PTPRM,SCN2B,SLC29A1,SMARCA1,TIMP2,ZNF532

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 PRELP

There's no related Drug.

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Cross referenced IDs for PRELP

* 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