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 OSBP
Basic gene info.Gene symbolOSBP
Gene nameoxysterol binding protein
SynonymsOSBP1
CytomapUCSC genome browser: 11q12-q13
Genomic locationchr11 :59341870-59383617
Type of geneprotein-coding
RefGenesNM_002556.2,
Ensembl idENSG00000110048
Descriptionoxysterol-binding protein 1
Modification date20141207
dbXrefs MIM : 167040
HGNC : HGNC
Ensembl : ENSG00000110048
HPRD : 01327
Vega : OTTHUMG00000167422
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OSBP
BioGPS: 5007
Gene Expression Atlas: ENSG00000110048
The Human Protein Atlas: ENSG00000110048
PathwayNCI Pathway Interaction Database: OSBP
KEGG: OSBP
REACTOME: OSBP
ConsensusPathDB
Pathway Commons: OSBP
MetabolismMetaCyc: OSBP
HUMANCyc: OSBP
RegulationEnsembl's Regulation: ENSG00000110048
miRBase: chr11 :59,341,870-59,383,617
TargetScan: NM_002556
cisRED: ENSG00000110048
ContextiHOP: OSBP
cancer metabolism search in PubMed: OSBP
UCL Cancer Institute: OSBP
Assigned class in ccmGDBC

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

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

Mutations for OSBP
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastOSBPchr115937782759377827chr115939393859393938
ovaryOSBPchr115935916659359186OSBPchr115936218059362200
ovaryOSBPchr115937838059378400DLG2chr118420092584200945
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows OSBP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP420837OSBP25146115938272459382845SRRM114249912499677124998784

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=43)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr11:59376014-59376014p.I255I3
chr11:59344432-59344432p.G709G2
chr11:59344448-59344448p.N704S2
chr11:59382804-59382804p.L112L2
chr11:59369301-59369301p.D278G2
chr11:59382832-59382832p.I102I2
chr11:59367978-59367978p.I434I2
chr11:59368300-59368300p.D391N2
chr11:59377994-59377994p.E144V2
chr11:59344413-59344413p.R716W2

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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
# sample41 62 4 1  1131  75110
# mutation41 62 4 1  1241  76113
nonsynonymous SNV31 51 3 1  841  5319
synonymous SNV1  11 1    4    23 4
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
chr11:59344432p.E250K2
chr11:59376031p.G709G2
chr11:59361714p.N148K1
chr11:59382832p.P687Q1
chr11:59344452p.R490C1
chr11:59368785p.E356Q1
chr11:59348978p.R107L1
chr11:59376069p.P685L1
chr11:59367978p.L447R1
chr11:59344479p.D352D1

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 OSBP 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 OSBP

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

ARCN1,CCDC186,C9orf41,CCNT1,COPB1,DDB1,EIF2AK3,
GTF2A1,IDE,IPP,OSBP,PAFAH1B2,PATL1,PPP4R2,
RSC1A1,SPTY2D1,STT3B,STX3,TMF1,UEVLD,ZFP91
ANAPC1,C9orf41,CLCN3,CNOT1,CSNK2A3,GIGYF2,GSK3B,
KDM3B,MPP5,OSBP,PPP4R2,RABGAP1,SBNO1,SKIV2L2,
SPG11,STT3B,TNKS,TUBGCP4,ZBTB44,ZNF41,ZNF770

ALDH6A1,ARCN1,ARHGAP32,CTNND1,DDB1,FAM160A1,HYOU1,
INCENP,MARK2,NCOR1,NIPAL3,OSBP,PAFAH1B2,PATL1,
PPFIA1,RSC1A1,SBNO1,SPTLC2,STT3A,ZDHHC5,ZFP91
AIM1,ARHGAP32,ATP6V1A,PRR14L,CNOT1,CPD,CSNK2A1,
CTR9,DCAF7,DNAJC16,DSP,FCGBP,KDM4A,KDM5B,
LARP4B,MAN2A1,MED14,OSBP,PLCH1,SPG11,SPTLC2
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 OSBP


There's no related Drug.
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Cross referenced IDs for OSBP
* 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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