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 PREB

Basic gene info.	Gene symbol	PREB
	Gene name	prolactin regulatory element binding
	Synonyms	SEC12
	Cytomap	UCSC genome browser: 2p23.3
	Genomic location	chr2 :27353624-27357542
	Type of gene	protein-coding
	RefGenes	NM_013388.4,
	Ensembl id	ENSG00000138073
	Description	mammalian guanine nucleotide exchange factor mSec12prolactin regulatory binding-element proteinprolactin regulatory element-binding protein
	Modification date	20141207
dbXrefs	MIM : 606395
	HGNC : HGNC
	Ensembl : ENSG00000138073
	HPRD : 16216
	Vega : OTTHUMG00000097076
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PREB
	BioGPS: 10113
	Gene Expression Atlas: ENSG00000138073
	The Human Protein Atlas: ENSG00000138073
Pathway	NCI Pathway Interaction Database: PREB
	KEGG: PREB
	REACTOME: PREB
	ConsensusPathDB
	Pathway Commons: PREB
Metabolism	MetaCyc: PREB
	HUMANCyc: PREB
Regulation	Ensembl's Regulation: ENSG00000138073
	miRBase: chr2 :27,353,624-27,357,542
	TargetScan: NM_013388
	cisRED: ENSG00000138073
Context	iHOP: PREB
	cancer metabolism search in PubMed: PREB
	UCL Cancer Institute: PREB
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PREB
	Familial Cancer Database: PREB

* 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_PROTEINS

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

Mutations for PREB

* 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 PREB 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
DB179712	ORC5	1	41	7	103770660	103770700	PREB	42	544	2	27356443	27357510
AA467840	PREB	7	107	2	27356056	27356156	PREB	104	256	2	27355503	27355770
AW968190	PREB	73	225	2	27355503	27355770	PREB	222	322	2	27356056	27356156
AA468217	PREB	8	108	2	27356056	27356156	PREB	105	222	2	27355503	27355736
AA467896	PREB	7	159	2	27355503	27355770	PREB	156	256	2	27356056	27356156

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	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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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
chr2:27354694-27354694	p.L335L	3
chr2:27354540-27354540	p.R387W	2
chr2:27354887-27354887	p.F330L	2
chr2:27356449-27356449	p.L92L	2
chr2:27354627-27354627	p.G358R	1
chr2:27355991-27355991	p.V180V	1
chr2:27355105-27355105	p.D307N	1
chr2:27356590-27356590	p.?	1
chr2:27355501-27355501	p.S241F	1
chr2:27354630-27354630	p.R357C	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	1	1	3					1			10	2	1			2	5	1	4
# mutation	1	1	1	3					1			10	2	1			2	5	1	5
nonsynonymous SNV	1		1	3					1			7	1	1			2	2		4
synonymous SNV		1										3	1					3	1	1

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
chr2:27354540	p.R387W	2
chr2:27354630	p.R251R	1
chr2:27355197	p.G363G	1
chr2:27356508	p.R246H	1
chr2:27354640	p.G358R	1
chr2:27355204	p.R246C	1
chr2:27356559	p.R357S	1
chr2:27354655	p.S241F	1
chr2:27355223	p.P353P	1
chr2:27357164	p.D348D	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 PREB 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 PREB

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


AUP1,BOLA3,ATRAID,CCT7,COPE,DPY30,EIF2B4, FAM58A,HS1BP3,LSM4,MOGS,NRBP1,OST4,PPM1G, PREB,SF3B14,SLC5A6,SNX17,TBRG4,TMEM214,TSSC1	ACTR1A,ATG9A,AAMDC,PRADC1,DKFZp779M0652,HAGH,HSPB2, LSM10,MAP7D1,MECR,MSRB2,NPLOC4,PACS2,PREB, PRKACA,PSMD2,RILP,SLC25A20,STK40,SYNPO,TOMM40L

ACP1,BOLA3,CCT4,CCT7,FAM136A,GEMIN6,MEMO1, MRPL30,MRPL33,MYEOV2,NME1,OST4,PNO1,POLR2D, PREB,PSMD14,PTCD3,RPS7,SF3B14,SNRPG,TSSC1	HYPK,C19orf10,CDC123,EMC8,GLRX3,MRPL52,MRTO4, NME1,PFDN6,POP5,PRDX4,PREB,PSMD14,RAN, RPL26L1,RQCD1,SEC61B,SNRPB,SRPRB,SSR3,TOMM5

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 PREB

There's no related Drug.

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Cross referenced IDs for PREB

* 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