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 MUC12
Basic gene info.Gene symbolMUC12
Gene namemucin 12, cell surface associated
SynonymsMUC-11|MUC-12|MUC11
CytomapUCSC genome browser: 7q22
Genomic locationchr7 :100612903-100662230
Type of geneprotein-coding
RefGenesNM_001164462.1,
Ensembl idENSG00000205277
Descriptionmucin 11mucin-11mucin-12
Modification date20141207
dbXrefs MIM : 604609
HGNC : HGNC
Ensembl : ENSG00000205277
Vega : OTTHUMG00000157042
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MUC12
BioGPS: 10071
Gene Expression Atlas: ENSG00000205277
The Human Protein Atlas: ENSG00000205277
PathwayNCI Pathway Interaction Database: MUC12
KEGG: MUC12
REACTOME: MUC12
ConsensusPathDB
Pathway Commons: MUC12
MetabolismMetaCyc: MUC12
HUMANCyc: MUC12
RegulationEnsembl's Regulation: ENSG00000205277
miRBase: chr7 :100,612,903-100,662,230
TargetScan: NM_001164462
cisRED: ENSG00000205277
ContextiHOP: MUC12
cancer metabolism search in PubMed: MUC12
UCL Cancer Institute: MUC12
Assigned class in ccmGDBC

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Phenotypic Information for MUC12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MUC12
Familial Cancer Database: MUC12
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MUC12
MedGen: MUC12 (Human Medical Genetics with Condition)
ClinVar: MUC12
PhenotypeMGI: MUC12 (International Mouse Phenotyping Consortium)
PhenomicDB: MUC12

Mutations for MUC12
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasMUC12chr7100619868100619888MUC12chr7100624110100624130
pancreasMUC12chr7100636305100636505MUC12chr7100646425100646625
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 MUC12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG955820FLNB116835811237658116524MUC121633647100634934100635135
AW603439SYNE2279301146461366964613691MUC122845547100657290100661914

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 1  
GAIN (# sample)            1 1  
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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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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=391)
Stat. for Synonymous SNVs
(# total SNVs=115)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=7)

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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
chr7:100647548-100647548p.L4568F7
chr7:100647539-100647539p.S4565S6
chr7:100647276-100647276p.P4478T5
chr7:100612955-100612956p.T18_T19insA5
chr7:100643088-100643088p.I3082V5
chr7:100643155-100643155p.K3104I4
chr7:100637074-100637074p.R1077H4
chr7:100637605-100637605p.K1254T4
chr7:100634964-100634964p.P374T4
chr7:100647565-100647565p.S4574L4

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 13         2     1 20
# mutation 14         3     1 40
nonsynonymous SNV 12         3     1 27
synonymous SNV 2                 13
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
chr7:100634368p.T175M2
chr7:100646595p.P4251S2
chr7:100634997p.A15T1
chr7:100647960p.K492K1
chr7:100635842p.S3580I1
chr7:100656367p.H4909R1
chr7:100612946p.T73A1
chr7:100644583p.Q547K1
chr7:100635033p.S3593S1
chr7:100648001p.S4912L1

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 MUC12 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 MUC12

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

TMEM51-AS1,GNG3,IGFL2,KCNA10,KLK7,LY6H,MUC12,
MUC4,MYBPHL,NACAD,NEFL,NMU,OR10Q1,RS1,
SLC6A7,SPATA19,EPPIN,TPPP3,TTC9B,UPK2,WBSCR28
BASP1,BATF3,MEDAG,CCDC109B,CCIN,CD70,CLEC3B,
CMTM3,CRIP1,DBN1,EMP3,GLIPR2,LOXL1,METRNL,
MFRP,MUC12,NCF4,SH3BGRL3,THBS3,TMSB4XP8,TPPP3

BTNL3,CEACAM5,CLDN23,CLDN3,DHRS11,TMEM236,NXPE4,
FOXD2,LRRFIP2,MCOLN2,MUC12,MYO15B,PDE6A,PPP1R14C,
RPL10L,SEPP1,TFCP2L1,TM9SF4,TMEM82,ZBTB7A,ZSWIM1
ATP13A3,C2CD3,C3orf52,CLCN3,EPB41L4A,GALNT5,HIPK1,
IWS1,JPH1,LMNA,LOC100129637,KMT2B___KMT2D,MUC12,MUC4,
MYOF,PKD1L1,PVR,QSOX1,SETD8,TPD52L3,ZSCAN12P1
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 MUC12


There's no related Drug.
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Cross referenced IDs for MUC12
* 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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