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 BMP1

Basic gene info.	Gene symbol	BMP1
	Gene name	bone morphogenetic protein 1
	Synonyms	OI13\|PCOLC\|PCP\|PCP2\|TLD
	Cytomap	UCSC genome browser: 8p21.3
	Genomic location	chr8 :22022652-22058996
	Type of gene	protein-coding
	RefGenes	NM_001199.3, NM_006129.4,NR_033403.1,NR_033404.1,NM_006128.2, NM_006130.1,NM_006131.1,NM_006132.1,
	Ensembl id	ENSG00000168487
	Description	mammalian tolloid proteinprocollagen C-endopeptidaseprocollagen C-proteinase 3
	Modification date	20141207
dbXrefs	MIM : 112264
	HGNC : HGNC
	Ensembl : ENSG00000168487
	HPRD : 00209
	Vega : OTTHUMG00000097761
Protein	UniProt: P13497 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BMP1
	BioGPS: 649
	Gene Expression Atlas: ENSG00000168487
	The Human Protein Atlas: ENSG00000168487
Pathway	NCI Pathway Interaction Database: BMP1
	KEGG: BMP1
	REACTOME: BMP1
	ConsensusPathDB
	Pathway Commons: BMP1
Metabolism	MetaCyc: BMP1
	HUMANCyc: BMP1
Regulation	Ensembl's Regulation: ENSG00000168487
	miRBase: chr8 :22,022,652-22,058,996
	TargetScan: NM_001199
	cisRED: ENSG00000168487
Context	iHOP: BMP1
	cancer metabolism search in PubMed: BMP1
	UCL Cancer Institute: BMP1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of BMP1 in cancer cell metabolism	1. Palmieri D, Fitzgerald D, Shreeve SM, Hua E, Bronder JL, et al. (2009) Analyses of resected human brain metastases of breast cancer reveal the association between up-regulation of hexokinase 2 and poor prognosis. Mol Cancer Res 7: 1438-1445. doi: 10.1158/1541-7786.MCR-09-0234. pmid: 2746883 go to article

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Phenotypic Information for BMP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: BMP1
	Familial Cancer Database: BMP1

* 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_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM

Others
OMIM	112264; gene. 112264; gene. 614856; phenotype. 614856; phenotype.
Orphanet	216812; Osteogenesis imperfecta type 3. 216812; Osteogenesis imperfecta type 3.
Disease	KEGG Disease: BMP1
	MedGen: BMP1 (Human Medical Genetics with Condition)
	ClinVar: BMP1
Phenotype	MGI: BMP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: BMP1

Mutations for BMP1

* 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 BMP1 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
BF737796	BMP1	9	347	8	22037967	22052046	MALL	345	430	2	110841958	110842043
AA452720	BMP1	3	128	8	22052259	22052390	BMP1	123	474	8	22034121	22035467
BQ370786	KCTD10	9	373	12	109888610	109888974	BMP1	369	475	8	22058288	22058394

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=61)	Stat. for Synonymous SNVs (# total SNVs=21)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=4)

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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
chr8:22054259-22054260	p.N614fs*21	3
chr8:22066962-22066962	p.C860C	3
chr8:22064409-22064409	p.T759N	2
chr8:22052315-22052315	p.R508C	2
chr8:22054230-22054230	p.S601S	2
chr8:22052228-22052228	p.?	2
chr8:22037901-22037901	p.D328H	2
chr8:22034502-22034502	p.G194R	2
chr8:22033756-22033756	p.A121A	2
chr8:22053004-22053004	p.G557R	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=3

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	3	1		12	1			1	2	1		7	1	3	1	1	11	11		16
# mutation	3	1		13	1			1	2	1		9	1	3	1	1	12	12		23
nonsynonymous SNV		1		8				1	2	1		9		2	1		4	7		18
synonymous SNV	3			5	1								1	1		1	8	5		5

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
chr8:22066962	p.C860C	2
chr8:22033822	p.K694R,BMP1	1
chr8:22052301	p.R865W	1
chr8:22064891	p.E35D,BMP1	1
chr8:22037329	p.G280D,BMP1	1
chr8:22054225	p.F428Y,BMP1	1
chr8:22023023	p.V542F,BMP1	1
chr8:22051673	p.R712L	1
chr8:22054907	p.V868M	1
chr8:22034084	p.R64R,BMP1	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 BMP1 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 BMP1

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


ADAMTS14,BMP1,CD248,COL16A1,COL18A1,COL5A3,COL6A1, COL6A2,EFEMP2,ELFN1,EMILIN1,EMP3,LEPRE1,MMP14, MRC2,OLFML2B,PCOLCE,RCN3,RFX8,SERPINH1,THY1	ACVRL1,ADAMTS2,ADAMTS7,AP2A2,BMP1,CD248,COL6A1, COL6A2,CTSL,EMILIN2,COLGALT1,HTRA3,ITGA5,MCOLN1, MGAT1,PLXND1,RCN3,RENBP,SERPINH1,STAB1,TCN2

ADAMTS7,BMP1,CERCAM,COL12A1,COL1A1,COL1A2,COL3A1, COL5A1,COL5A2,COL6A1,COL6A2,COL6A3,LEPRE1,MMP14, MRC2,PCOLCE,PODNL1,PXDN,RCN3,SPARC,ZNF469	ARHGEF11,BMP1,CLIP2,CLSTN1,CNNM4,DAB2IP,DNM2, GRAMD4,INF2,JUP,MINK1,NR2F6,PLXNB2,RAB40C, RXRA,SIPA1L3,SLC9A1,TJP3,TMEM63B,WWP2,ZBTB7A

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 BMP1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P13497; -.
Chemistry	ChEMBL	CHEMBL3898; -.
Chemistry	BindingDB	P13497; -.
Chemistry	ChEMBL	CHEMBL3898; -.
Organism-specific databases	PharmGKB	PA25377; -.
Organism-specific databases	PharmGKB	PA25377; -.
Organism-specific databases	CTD	649; -.
Organism-specific databases	CTD	649; -.

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
DB01033	bone morphogenetic protein 1	approved	Mercaptopurine
DB00563	bone morphogenetic protein 1	approved	Methotrexate

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Cross referenced IDs for BMP1

* 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