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 OSBP

Basic gene info.	Gene symbol	OSBP
	Gene name	oxysterol binding protein
	Synonyms	OSBP1
	Cytomap	UCSC genome browser: 11q12-q13
	Genomic location	chr11 :59341870-59383617
	Type of gene	protein-coding
	RefGenes	NM_002556.2,
	Ensembl id	ENSG00000110048
	Description	oxysterol-binding protein 1
	Modification date	20141207
dbXrefs	MIM : 167040
	HGNC : HGNC
	Ensembl : ENSG00000110048
	HPRD : 01327
	Vega : OTTHUMG00000167422
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_OSBP
	BioGPS: 5007
	Gene Expression Atlas: ENSG00000110048
	The Human Protein Atlas: ENSG00000110048
Pathway	NCI Pathway Interaction Database: OSBP
	KEGG: OSBP
	REACTOME: OSBP
	ConsensusPathDB
	Pathway Commons: OSBP
Metabolism	MetaCyc: OSBP
	HUMANCyc: OSBP
Regulation	Ensembl's Regulation: ENSG00000110048
	miRBase: chr11 :59,341,870-59,383,617
	TargetScan: NM_002556
	cisRED: ENSG00000110048
Context	iHOP: OSBP
	cancer metabolism search in PubMed: OSBP
	UCL Cancer Institute: OSBP
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	OSBP	chr11	59377827	59377827		chr11	59393938	59393938
ovary	OSBP	chr11	59359166	59359186	OSBP	chr11	59362180	59362200
ovary	OSBP	chr11	59378380	59378400	DLG2	chr11	84200925	84200945

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)

Related fusion transcripts : go to Chitars2.0

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

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

BP420837

OSBP

146

59382724

59382845

SRRM1

142

499

24996771

24998784

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=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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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
chr11:59376014-59376014	p.I255I	3
chr11:59344448-59344448	p.N704S	2
chr11:59382804-59382804	p.L112L	2
chr11:59369301-59369301	p.D278G	2
chr11:59382832-59382832	p.I102I	2
chr11:59367978-59367978	p.I434I	2
chr11:59368300-59368300	p.D391N	2
chr11:59377994-59377994	p.E144V	2
chr11:59344413-59344413	p.R716W	2
chr11:59344432-59344432	p.G709G	2

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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	4	1		6	2		4		1			11	3	1			7	5	1	10
# mutation	4	1		6	2		4		1			12	4	1			7	6	1	13
nonsynonymous SNV	3	1		5	1		3		1			8	4	1			5	3	1	9
synonymous SNV	1			1	1		1					4					2	3		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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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
chr11:59344432	p.E250K	2
chr11:59376031	p.G709G	2
chr11:59376069	p.E442D	1
chr11:59348978	p.S345F	1
chr11:59367978	p.I102I	1
chr11:59368788	p.R667R	1
chr11:59344479	p.I434I	1
chr11:59376080	p.L308L	1
chr11:59349008	p.T645M	1
chr11:59367985	p.S432C	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 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

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


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

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 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