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 BBOX1

Basic gene info.	Gene symbol	BBOX1
	Gene name	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1
	Synonyms	BBH\|BBOX\|G-BBH\|gamma-BBH
	Cytomap	UCSC genome browser: 11p14.2
	Genomic location	chr11 :27062508-27149354
	Type of gene	protein-coding
	RefGenes	NM_003986.2,
	Ensembl id	ENSG00000129151
	Description	gamma-butyrobetaine dioxygenasegamma-butyrobetaine hydroxylasegamma-butyrobetaine,2-oxoglutarate dioxygenase 1
	Modification date	20141207
dbXrefs	MIM : 603312
	HGNC : HGNC
	Ensembl : ENSG00000129151
	HPRD : 04498
	Vega : OTTHUMG00000166121
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BBOX1
	BioGPS: 8424
	Gene Expression Atlas: ENSG00000129151
	The Human Protein Atlas: ENSG00000129151
Pathway	NCI Pathway Interaction Database: BBOX1
	KEGG: BBOX1
	REACTOME: BBOX1
	ConsensusPathDB
	Pathway Commons: BBOX1
Metabolism	MetaCyc: BBOX1
	HUMANCyc: BBOX1
Regulation	Ensembl's Regulation: ENSG00000129151
	miRBase: chr11 :27,062,508-27,149,354
	TargetScan: NM_003986
	cisRED: ENSG00000129151
Context	iHOP: BBOX1
	cancer metabolism search in PubMed: BBOX1
	UCL Cancer Institute: BBOX1
Assigned class in ccmGDB	C

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Phenotypic Information for BBOX1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: BBOX1
	Familial Cancer Database: BBOX1

* 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_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: BBOX1
	MedGen: BBOX1 (Human Medical Genetics with Condition)
	ClinVar: BBOX1
Phenotype	MGI: BBOX1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BBOX1

Mutations for BBOX1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	BBOX1	chr11	27062746	27062766	CD300E	chr17	72618661	72618681
ovary	BBOX1	chr11	27123872	27123892		chr11	26207039	26207059
pancreas	BBOX1	chr11	27072869	27072889	BBOX1	chr11	27074711	27074731
pancreas	BBOX1	chr11	27080800	27080820	BBOX1	chr11	27083039	27083059
pancreas	BBOX1	chr11	27096086	27096106	BBOX1	chr11	27074774	27074794
pancreas	BBOX1	chr11	27122963	27122983	BBOX1	chr11	27124483	27124503
pancreas	BBOX1	chr11	27127774	27127974		chr11	27177551	27177751
pancreas	BBOX1	chr11	27141989	27142009	LGR4	chr11	27425891	27425911

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 BBOX1 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
BF750399	BBOX1	1	196	11	27113989	27114184	KLK7	193	305	19	51483708	51485099
AW798404	BBOX1	76	103	11	27089771	27089800	FOS	101	224	14	75748601	75748724

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=35)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr11:27114788-27114788	p.H136H	3
chr11:27078827-27078827	p.A100D	2
chr11:27114906-27114906	p.F176V	2
chr11:27137012-27137012	p.V183M	2
chr11:27148884-27148884	p.R350C	2
chr11:27148982-27148982	p.R382R	2
chr11:27114883-27114883	p.R168K	1
chr11:27148986-27148986	p.E384K	1
chr11:27077154-27077154	p.D59E	1
chr11:27141378-27141378	p.K274K	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	2	1	1	6	1		2		1			7	3				6	3		2
# mutation	2	1	2	5	1		2		2			7	3				6	3		2
nonsynonymous SNV	1		2	4			1		2			6	2				3	2		1
synonymous SNV	1	1		1	1		1					1	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
chr11:27148982	p.F176V	2
chr11:27114906	p.R382R	2
chr11:27148880	p.C113C	1
chr11:27078769	p.A312D	1
chr11:27141369	p.E128K	1
chr11:27148881	p.E325K	1
chr11:27078781	p.G166W	1
chr11:27141378	p.G348G	1
chr11:27148882	p.R349R	1
chr11:27078786	p.D188H	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 BBOX1 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 BBOX1

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


ANXA1,BBOX1,CEBPB,CFI,CHI3L1,CNTNAP3,DEFB1, CCDC71L,GABRP,HAPLN3,LYN,MOB3B,MPZL2,PAK3, PLCG2,PROM1,RARRES1,TANK,TIGD2,TINAGL1,TLR2	ALDH1A3,ARFGAP3,BBOX1,PLEKHS1,EVA1C,CA13,CDCP1, CMTM7,CXCL16,GRAMD2,LOC100190939,LRRC4C,LTF,PROM1, RARRES1,RASGEF1A,SLC34A2,SLPI,STAC2,TC2N,VGLL1

ANGPTL5,BBOX1,C17orf78,CALCB,CLDN22,CYP17A1,CYP7A1, EPB42,GLIPR1,HSD17B13,INSC,LBP,MRAP,NLRP6, PTCHD3,SERPINE3,SLC7A9,SPAM1,TAAR1,TBX3,TMEM229A	ACADL,BBOX1,LINC00301,C1orf194,C1QL1,FAM228A,CLPSL2, SPATA31D1,GLYAT,GTF2A1L,IFNA2,KLHDC8A,MGC2889,OR52D1, PCDHB18,S100G,SCN1A,TAAR8,TF,USP17L9P,WSCD2

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 BBOX1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00126	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	approved; nutraceutical	Vitamin C
DB00139	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	approved; nutraceutical	Succinic acid
DB00145	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	approved; nutraceutical	Glycine

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Cross referenced IDs for BBOX1

* 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