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 CHRM3
Basic gene info.Gene symbolCHRM3
Gene namecholinergic receptor, muscarinic 3
SynonymsEGBRS|HM3
CytomapUCSC genome browser: 1q43
Genomic locationchr1 :239792372-240072717
Type of geneprotein-coding
RefGenesNM_000740.2,
Ensembl idENSG00000133019
Descriptionacetylcholine receptor, muscarinic 3m3 muscarinic receptormuscarinic acetylcholine receptor M3
Modification date20141207
dbXrefs MIM : 118494
HGNC : HGNC
Ensembl : ENSG00000133019
HPRD : 00329
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHRM3
BioGPS: 1131
Gene Expression Atlas: ENSG00000133019
The Human Protein Atlas: ENSG00000133019
PathwayNCI Pathway Interaction Database: CHRM3
KEGG: CHRM3
REACTOME: CHRM3
ConsensusPathDB
Pathway Commons: CHRM3
MetabolismMetaCyc: CHRM3
HUMANCyc: CHRM3
RegulationEnsembl's Regulation: ENSG00000133019
miRBase: chr1 :239,792,372-240,072,717
TargetScan: NM_000740
cisRED: ENSG00000133019
ContextiHOP: CHRM3
cancer metabolism search in PubMed: CHRM3
UCL Cancer Institute: CHRM3
Assigned class in ccmGDBC

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Phenotypic Information for CHRM3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHRM3
Familial Cancer Database: CHRM3
* 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_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CHRM3
MedGen: CHRM3 (Human Medical Genetics with Condition)
ClinVar: CHRM3
PhenotypeMGI: CHRM3 (International Mouse Phenotyping Consortium)
PhenomicDB: CHRM3

Mutations for CHRM3
* 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
NSCHRM3chr1239813421239813421CHRM3chr1240054640240054640
ovaryCHRM3chr1239885458239885478CHRM3chr1239883247239883267
ovaryCHRM3chr1239895625239895645CHRM3chr1239895913239895933
ovaryCHRM3chr1239970080239970100CHRM3chr1239970186239970206
pancreasCHRM3chr1239822524239822544chr1240902950240902970
pancreasCHRM3chr1239895262239895462CHRM3chr1239895918239896118
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 CHRM3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV402170CHRM3121271239648846239648962CHRM31273301239651538239651741
BX487190STATH7342947086660870868170CHRM34246421239615753239615972
BE149291GAS7143331799768609977178CHRM33264611239906900239907035
AW367527PDCD4119310112658410112658603CHRM31893581239756964239757133
AI205037FBXL182254755212545521506CHRM32543481240031715240031809
BE143319CHRM3181031239855197239855286CHRM31005531239844738239845191
AW812006SPG11180323154487611644876259CHRM33205281239903756239903964

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 # sample8  1  1 1 1    13
GAIN (# sample)7  1      1    13
LOSS (# sample)1     1 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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=92)		Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=2)		Stat. for Insertions
(# total SNVs=2)

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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
chr1:240071233-240071233p.V161A4
chr1:240071275-240071275p.T175M3
chr1:240070919-240070919p.T56T3
chr1:240072444-240072444p.K567fs*>243
chr1:240071128-240071128p.T126M3
chr1:240070879-240070879p.S43Y3
chr1:240072033-240072033p.P428S3
chr1:240071520-240071520p.E257K2
chr1:240071276-240071276p.T175T2
chr1:240072078-240072078p.V443I2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample43 183 4 2  2037  2811111
# mutation63 143 4 2  2237  3211110
nonsynonymous SNV41 101 3 2  1635  199 7
synonymous SNV22 42 1    6 2  13213
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
chr1:240071233p.V161A4
chr1:240070879p.S43F3
chr1:240072213p.T56T2
chr1:240071510p.K488E2
chr1:240072215p.K488K2
chr1:240071532p.R584H2
chr1:240070919p.R253S2
chr1:240071103p.R261C2
chr1:240072078p.E347E2
chr1:240071792p.G118R2

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 CHRM3 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 CHRM3

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

APBA1,BCL11A,CDH19,CHRM3,EPHB1,EPHB3,ETV5,
GALNT13,GPR125,GPR161,ITGA6,ITGA9,LRP6,OTX1,
ROPN1B,SFRP1,SOX10,SOX6,TMX4,TRIM2,ZNF462		ASIC1,APBA2,AQP5,VSTM5,B3GALT5-AS1,CHRM1,CHRM3,
ETV3L,FAM196B,FAM81A,FOLH1,GPR156,HS3ST4,IGSF5,
KCNK5,NALCN,PHLPP1,ROPN1,SOX8,TGFA,TMEM213

ADSS,ARID4B,BCL9,CHRM3,EFNA4,GRAMD1A,KDM5B,
LGR5,MAML2,PCNXL2,PGAP1,PI4KB,PMEPA1,POGK,
DESI2,RUNX1,SEC14L4,SOX4,TGFBI,TLR4,TP53BP2		AR,ARHGEF17,CACNA1C,CACNA1H,CD109,CHRM3,CNTNAP1,
COL4A1,EMILIN1,FAT4,GPR156,ITGB3,KCNB1,KCNQ4,
PRUNE2,PTPN14,RYR2,SPEG,TMTC2,TNS1,ZFHX4
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 CHRM3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00185cholinergic receptor, muscarinic 3approvedCevimeline
DB00193cholinergic receptor, muscarinic 3approved; investigationalTramadol
DB00202cholinergic receptor, muscarinic 3approvedSuccinylcholine
DB00246cholinergic receptor, muscarinic 3approvedZiprasidone
DB00280cholinergic receptor, muscarinic 3approvedDisopyramide
DB00321cholinergic receptor, muscarinic 3approvedAmitriptyline
DB00332cholinergic receptor, muscarinic 3approvedIpratropium bromide
DB00334cholinergic receptor, muscarinic 3approved; investigationalOlanzapine
DB00340cholinergic receptor, muscarinic 3approvedMetixene
DB00342cholinergic receptor, muscarinic 3approved; withdrawnTerfenadine
DB00363cholinergic receptor, muscarinic 3approvedClozapine
DB00376cholinergic receptor, muscarinic 3approvedTrihexyphenidyl
DB00383cholinergic receptor, muscarinic 3approvedOxyphencyclimine
DB00387cholinergic receptor, muscarinic 3approvedProcyclidine
DB00420cholinergic receptor, muscarinic 3approvedPromazine
DB00424cholinergic receptor, muscarinic 3approvedHyoscyamine
DB00434cholinergic receptor, muscarinic 3approvedCyproheptadine
DB00458cholinergic receptor, muscarinic 3approvedImipramine
DB00462cholinergic receptor, muscarinic 3approvedMethylscopolamine
DB00496cholinergic receptor, muscarinic 3approved; investigationalDarifenacin
DB00505cholinergic receptor, muscarinic 3approvedTridihexethyl
DB00517cholinergic receptor, muscarinic 3approvedAnisotropine Methylbromide
DB00540cholinergic receptor, muscarinic 3approvedNortriptyline
DB00572cholinergic receptor, muscarinic 3approvedAtropine
DB00622cholinergic receptor, muscarinic 3approvedNicardipine
DB00715cholinergic receptor, muscarinic 3approved; investigationalParoxetine
DB00725cholinergic receptor, muscarinic 3approvedHomatropine Methylbromide
DB00729cholinergic receptor, muscarinic 3approvedDiphemanil Methylsulfate
DB00747cholinergic receptor, muscarinic 3approvedScopolamine
DB00767cholinergic receptor, muscarinic 3approvedBenzquinamide
DB00777cholinergic receptor, muscarinic 3approvedPropiomazine
DB00809cholinergic receptor, muscarinic 3approvedTropicamide
DB00835cholinergic receptor, muscarinic 3approvedBrompheniramine
DB00934cholinergic receptor, muscarinic 3approvedMaprotiline
DB01036cholinergic receptor, muscarinic 3approved; investigationalTolterodine
DB01062cholinergic receptor, muscarinic 3approved; investigationalOxybutynin
DB01069cholinergic receptor, muscarinic 3approvedPromethazine
DB01085cholinergic receptor, muscarinic 3approvedPilocarpine
DB01142cholinergic receptor, muscarinic 3approvedDoxepin
DB01151cholinergic receptor, muscarinic 3approvedDesipramine
DB01224cholinergic receptor, muscarinic 3approvedQuetiapine
DB01226cholinergic receptor, muscarinic 3approvedMivacurium
DB01231cholinergic receptor, muscarinic 3approvedDiphenidol
DB01238cholinergic receptor, muscarinic 3approved; investigationalAripiprazole
DB01239cholinergic receptor, muscarinic 3approvedChlorprothixene
DB01337cholinergic receptor, muscarinic 3approvedPancuronium
DB01338cholinergic receptor, muscarinic 3approvedPipecuronium
DB01403cholinergic receptor, muscarinic 3approvedMethotrimeprazine
DB01409cholinergic receptor, muscarinic 3approvedTiotropium
DB01591cholinergic receptor, muscarinic 3approvedSolifenacin
DB01625cholinergic receptor, muscarinic 3approvedIsopropamide
DB04843cholinergic receptor, muscarinic 3approvedMepenzolate
DB06702cholinergic receptor, muscarinic 3approvedFesoterodine
DB06709cholinergic receptor, muscarinic 3approvedMethacholine


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Cross referenced IDs for CHRM3
* 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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