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 PREB
Basic gene info.Gene symbolPREB
Gene nameprolactin regulatory element binding
SynonymsSEC12
CytomapUCSC genome browser: 2p23.3
Genomic locationchr2 :27353624-27357542
Type of geneprotein-coding
RefGenesNM_013388.4,
Ensembl idENSG00000138073
Descriptionmammalian guanine nucleotide exchange factor mSec12prolactin regulatory binding-element proteinprolactin regulatory element-binding protein
Modification date20141207
dbXrefs MIM : 606395
HGNC : HGNC
Ensembl : ENSG00000138073
HPRD : 16216
Vega : OTTHUMG00000097076
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PREB
BioGPS: 10113
Gene Expression Atlas: ENSG00000138073
The Human Protein Atlas: ENSG00000138073
PathwayNCI Pathway Interaction Database: PREB
KEGG: PREB
REACTOME: PREB
ConsensusPathDB
Pathway Commons: PREB
MetabolismMetaCyc: PREB
HUMANCyc: PREB
RegulationEnsembl's Regulation: ENSG00000138073
miRBase: chr2 :27,353,624-27,357,542
TargetScan: NM_013388
cisRED: ENSG00000138073
ContextiHOP: PREB
cancer metabolism search in PubMed: PREB
UCL Cancer Institute: PREB
Assigned class in ccmGDBC

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Phenotypic Information for PREB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

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

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 PREB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB179712ORC51417103770660103770700PREB4254422735644327357510
AA467840PREB710722735605627356156PREB10425622735550327355770
AW968190PREB7322522735550327355770PREB22232222735605627356156
AA468217PREB810822735605627356156PREB10522222735550327355736
AA467896PREB715922735550327355770PREB15625622735605627356156

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=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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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
chr2:27354694-27354694p.L335L3
chr2:27354540-27354540p.R387W2
chr2:27354887-27354887p.F330L2
chr2:27356449-27356449p.L92L2
chr2:27354302-27354302p.A412T1
chr2:27355580-27355580p.R215W1
chr2:27354688-27354688p.Y337Y1
chr2:27356140-27356140p.E131K1
chr2:27355197-27355197p.Q276R1
chr2:27354338-27354338p.G400W1

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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
# sample1113    1  1021  2514
# mutation1113    1  1021  2515
nonsynonymous SNV1 13    1  711  22 4
synonymous SNV 1         31    311
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
chr2:27354540p.R387W2
chr2:27354338p.Q276P1
chr2:27357185p.A12A1
chr2:27354887p.R386Q1
chr2:27355487p.L274M1
chr2:27357254p.H381Y1
chr2:27355105p.V267V1
chr2:27355501p.G363G1
chr2:27354542p.R251R1
chr2:27355120p.G358R1

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 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

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

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
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 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



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