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 MUC4
Basic gene info.Gene symbolMUC4
Gene namemucin 4, cell surface associated
SynonymsASGP|HSA276359|MUC-4
CytomapUCSC genome browser: 3q29
Genomic locationchr3 :195473637-195538844
Type of geneprotein-coding
RefGenesNM_004532.5,
NM_018406.6,NM_138297.4,NM_138298.1,NM_138299.1,
Ensembl idENSG00000145113
Descriptionascites sialoglycoproteinmucin 4, tracheobronchialmucin-4pancreatic adenocarcinoma mucintestis mucintracheobronchial mucin
Modification date20141207
dbXrefs MIM : 158372
HGNC : HGNC
Ensembl : ENSG00000145113
HPRD : 11829
Vega : OTTHUMG00000151827
ProteinUniProt: Q99102
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MUC4
BioGPS: 4585
Gene Expression Atlas: ENSG00000145113
The Human Protein Atlas: ENSG00000145113
PathwayNCI Pathway Interaction Database: MUC4
KEGG: MUC4
REACTOME: MUC4
ConsensusPathDB
Pathway Commons: MUC4
MetabolismMetaCyc: MUC4
HUMANCyc: MUC4
RegulationEnsembl's Regulation: ENSG00000145113
miRBase: chr3 :195,473,637-195,538,844
TargetScan: NM_004532
cisRED: ENSG00000145113
ContextiHOP: MUC4
cancer metabolism search in PubMed: MUC4
UCL Cancer Institute: MUC4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MUC4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MUC4
Familial Cancer Database: MUC4
* 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 158372; gene.
158372; gene.
Orphanet
DiseaseKEGG Disease: MUC4
MedGen: MUC4 (Human Medical Genetics with Condition)
ClinVar: MUC4
PhenotypeMGI: MUC4 (International Mouse Phenotyping Consortium)
PhenomicDB: MUC4

Mutations for MUC4
* 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
central_nervous_systemMUC4chr3195499188195499188MUC4chr3195499969195499969
central_nervous_systemMUC4chr3195502833195502833MUC4chr3195504730195504730
NSMUC4chr3195502794195502794MUC4chr3195503226195503226
ovaryMUC4chr3195486769195486789chr3196324135196324155
ovaryMUC4chr3195498236195498436MUC4chr3195497741195497941
ovaryMUC4chr3195506927195507127MUC4chr3195510642195510842
ovaryMUC4chr3195506979195507179MUC4chr3195510638195510838
pancreasMUC4chr3195512087195512287MUC4chr3195506660195506860
pancreasMUC4chr3195512104195512304MUC4chr3195507016195507216
pancreasMUC4chr3195513095195513295MUC4chr3195514906195515106
pancreasMUC4chr3195515227195515427MUC4chr3195506649195506849
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 MUC4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG015132VPS72152031151149313151149497MUC41942733195515498195515577
BG984966CLDN4112377324585873245980MUC41174233195516287195516593
DA435621MUC411343195477236195477374MUC41305673195487821195489124
BQ689257MUC43334433195515054195515492MAGEF14407863184428153184428499
AW391858LMO71189137643064876432149MUC41825203195530516195530853
BQ689139MUC43334433195515054195515492MAGEF14407873184428156184428499
AW391853LMO71189137643064876432151MUC41825173195530516195530852

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 # sample1         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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=85)
Stat. for Synonymous SNVs
(# total SNVs=31)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr3:195492231-195492231p.R334W3
chr3:195487898-195487898p.N666fs*83
chr3:195493607-195493607p.F279F3
chr3:195487765-195487765p.N710N3
chr3:195481125-195481125p.A860D2
chr3:195491945-195491945p.R380Q2
chr3:195490907-195490907p.?2
chr3:195481161-195481161p.P848L2
chr3:195492266-195492266p.R322H2
chr3:195492211-195492211p.W340*2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample56434116 13 763 16206163540 42
# mutation57034913 13 1043 24266164855 68
nonsynonymous SNV35122910 8 813 19165 43835 46
synonymous SNV2191203 5 23  5101121020 22
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
chr3:195505867p.V4195D6
chr3:195505836p.H4205Q6
chr3:195506597p.H3837Q5
chr3:195506940p.P3952S5
chr3:195505855p.S4199Y4
chr3:195505811p.T4214A4
chr3:195505772p.V4227L4
chr3:195511525p.E279K3
chr3:195516064p.A2310P3
chr3:195516435p.D2309G3

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 MUC4 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 MUC4

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

ADAMTSL4,BTN1A1,TMEM51-AS1,LINC00518,CACNA1E,HILS1,IGFL2,
KCNA10,KLK7,KRT9,MUC12,MUC4,MYBPHL,NEFL,
NMU,OR10Q1,RS1,SLC6A7,SPATA19,EPPIN,VGLL3
CXCL13,DEFB125,DIO2,FAM83A,HDGFL1,HELT,HS6ST2,
LHX9,LOC100130274,LOC100130933,LPAR3,MEPE,MUC4,OLAH,
OR10J5,OR2M3,PLA2G3,PSG8,PTHLH,SLC6A19,SLC9A4

ALDH1L1,CAPN5,CASP7,CES3,CREB3L1,ERN2,GNAQ,
HK2,ITM2C,KIAA0513,KLF4,MRAP2,MUC4,NR3C2,
PIGR,SLC22A23,SLC44A4,SPTLC2,ST3GAL4,VSIG2,ZBTB7C
ABL2,ATR,FAM208B,CDK12,E2F3,FASN,JPH1,
KIAA1244,KIF14,LARP1,LMNB2,MDN1,MKI67,MUC4,
MUC5B,MYBBP1A,PDCD11,SLC7A1,SRRT,UGGT1,WHSC1
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 MUC4


There's no related Drug.
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Cross referenced IDs for MUC4
* 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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