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 BMP1
Basic gene info.Gene symbolBMP1
Gene namebone morphogenetic protein 1
SynonymsOI13|PCOLC|PCP|PCP2|TLD
CytomapUCSC genome browser: 8p21.3
Genomic locationchr8 :22022652-22058996
Type of geneprotein-coding
RefGenesNM_001199.3,
NM_006129.4,NR_033403.1,NR_033404.1,NM_006128.2,
NM_006130.1,NM_006131.1,NM_006132.1,
Ensembl idENSG00000168487
Descriptionmammalian tolloid proteinprocollagen C-endopeptidaseprocollagen C-proteinase 3
Modification date20141207
dbXrefs MIM : 112264
HGNC : HGNC
Ensembl : ENSG00000168487
HPRD : 00209
Vega : OTTHUMG00000097761
ProteinUniProt: P13497
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BMP1
BioGPS: 649
Gene Expression Atlas: ENSG00000168487
The Human Protein Atlas: ENSG00000168487
PathwayNCI Pathway Interaction Database: BMP1
KEGG: BMP1
REACTOME: BMP1
ConsensusPathDB
Pathway Commons: BMP1
MetabolismMetaCyc: BMP1
HUMANCyc: BMP1
RegulationEnsembl's Regulation: ENSG00000168487
miRBase: chr8 :22,022,652-22,058,996
TargetScan: NM_001199
cisRED: ENSG00000168487
ContextiHOP: BMP1
cancer metabolism search in PubMed: BMP1
UCL Cancer Institute: BMP1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of BMP1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM 112264; gene.
112264; gene.
614856; phenotype.
614856; phenotype.
Orphanet 216812; Osteogenesis imperfecta type 3.
216812; Osteogenesis imperfecta type 3.
DiseaseKEGG Disease: BMP1
MedGen: BMP1 (Human Medical Genetics with Condition)
ClinVar: BMP1
PhenotypeMGI: BMP1 (International Mouse Phenotyping Consortium)
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.

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 BMP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF737796BMP1934782203796722052046MALL3454302110841958110842043
AA452720BMP1312882205225922052390BMP112347482203412122035467
BQ370786KCTD10937312109888610109888974BMP136947582205828822058394

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
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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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=4

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check002.gifSomatic 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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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
chr8:22054259-22054260p.N614fs*213
chr8:22066962-22066962p.C860C3
chr8:22064409-22064409p.T759N2
chr8:22052315-22052315p.R508C2
chr8:22054230-22054230p.S601S2
chr8:22052228-22052228p.?2
chr8:22037901-22037901p.D328H2
chr8:22034502-22034502p.G194R2
chr8:22033756-22033756p.A121A2
chr8:22053004-22053004p.G557R2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 121  121 713111111 16
# mutation31 131  121 913111212 23
nonsynonymous SNV 1 8   121 9 21 47 18
synonymous SNV3  51       11 185 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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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
chr8:22066962p.C860C2
chr8:22033822p.K694R,BMP11
chr8:22052301p.R865W1
chr8:22064891p.E35D,BMP11
chr8:22037329p.G280D,BMP11
chr8:22054225p.F428Y,BMP11
chr8:22023023p.V542F,BMP11
chr8:22051673p.R712L1
chr8:22054907p.V868M1
chr8:22034084p.R64R,BMP11

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 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

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

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
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 BMP1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P13497; -.
ChemistryChEMBL CHEMBL3898; -.
ChemistryBindingDB P13497; -.
ChemistryChEMBL CHEMBL3898; -.
Organism-specific databasesPharmGKB PA25377; -.
Organism-specific databasesPharmGKB PA25377; -.
Organism-specific databasesCTD 649; -.
Organism-specific databasesCTD 649; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033bone morphogenetic protein 1approvedMercaptopurine
DB00563bone morphogenetic protein 1approvedMethotrexate


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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



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