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 MUC5B
Basic gene info.Gene symbolMUC5B
Gene namemucin 5B, oligomeric mucus/gel-forming
SynonymsMG1|MUC-5B|MUC5|MUC9
CytomapUCSC genome browser: 11p15.5
Genomic locationchr11 :1244294-1283406
Type of geneprotein-coding
RefGenesNM_002458.2,
Ensembl idENSG00000117983
Descriptioncervical mucin MUC5Bhigh molecular weight salivary mucin MG1mucin 5, subtype B, tracheobronchialmucin-5Bsublingual gland mucin
Modification date20141222
dbXrefs MIM : 600770
HGNC : HGNC
Ensembl : ENSG00000117983
Vega : OTTHUMG00000166494
ProteinUniProt: Q9HC84
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MUC5B
BioGPS: 727897
Gene Expression Atlas: ENSG00000117983
The Human Protein Atlas: ENSG00000117983
PathwayNCI Pathway Interaction Database: MUC5B
KEGG: MUC5B
REACTOME: MUC5B
ConsensusPathDB
Pathway Commons: MUC5B
MetabolismMetaCyc: MUC5B
HUMANCyc: MUC5B
RegulationEnsembl's Regulation: ENSG00000117983
miRBase: chr11 :1,244,294-1,283,406
TargetScan: NM_002458
cisRED: ENSG00000117983
ContextiHOP: MUC5B
cancer metabolism search in PubMed: MUC5B
UCL Cancer Institute: MUC5B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for MUC5B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MUC5B
Familial Cancer Database: MUC5B
* 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 178500; phenotype.
178500; phenotype.
600770; gene.
600770; gene.
Orphanet 171700; Diffuse panbronchiolitis.
171700; Diffuse panbronchiolitis.
2032; Idiopathic pulmonary fibrosis.
2032; Idiopathic pulmonary fibrosis.
DiseaseKEGG Disease: MUC5B
MedGen: MUC5B (Human Medical Genetics with Condition)
ClinVar: MUC5B
PhenotypeMGI: MUC5B (International Mouse Phenotyping Consortium)
PhenomicDB: MUC5B

Mutations for MUC5B
* 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
breastMUC5Bchr1112589801259380CARSchr1130521573052557
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 MUC5B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG955818MUC5B112101112713301271533MLEC20240312121139214121139415
BQ320008GHITM25123108590247485903812MUC5B1243381112636151263829

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
There's no copy number variation information in COSMIC data for this gene.

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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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=458)
Stat. for Synonymous SNVs
(# total SNVs=192)
Stat. for Deletions
(# total SNVs=20)
Stat. for Insertions
(# total SNVs=3)

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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
chr11:1253969-1253969p.V678V11
chr11:1258286-1258286p.D1063D7
chr11:1253976-1253976p.S681G7
chr11:1258283-1258283p.P1062P6
chr11:1263216-1263216p.T1702T5
chr11:1268931-1268931p.A3607A5
chr11:1264823-1264823p.L2238P4
chr11:1271321-1271321p.A4404G4
chr11:1261118-1261118p.G1225R4
chr11:1253980-1253980p.D682G4

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample73324310 241113347335124538657
# mutation73525412 2711134604151266616106
nonsynonymous SNV5192306 20193340314 24534471
synonymous SNV216 246 7 2 1201011 2127235
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
chr11:1261118p.G1225R4
chr11:1265872p.G2588R3
chr11:1271273p.T2053S2
chr11:1272524p.P4851L2
chr11:1271392p.A4428T2
chr11:1265053p.S4805C2
chr11:1269116p.A3700T2
chr11:1272662p.T3115T2
chr11:1265445p.S681G2
chr11:1267649p.T3131T2

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 MUC5B 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 MUC5B

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

ACLY,AMOT,COPA,EIF2AK3,GALNT7,GK3P,GLYCAM1,
GNA14,LRRC8B,MIA3,MUC5B,NSF,PCDHA5,PRKAA2,
SEC16A,SEC24A,SECISBP2L,SLC44A4,TP53INP2,UCP3,YPEL2
AURKB,BHLHA15,CIT,E2F2,ESPL1,EZH2,FANCA,
FANCI,GALNT5,HYOU1,IKBKE,KIF18B,KIF2C,LMNB1,
MUC5B,NUP210,ORC1,RAD54L,RFX5,SLC15A2,UHRF1

AGR2,ANG,BPIFB6,CD55,CKAP4,CREB3L1,FAM177B,
GALNT7,MROH2B,IGFALS,KDELR3,LIPF,MAP3K6,MLPH,
MUC5B,PDIA2,PGC,QSOX1,SLC39A7,SPDEF,UAP1
ACAN,ADAMTS15,AQPEP,ARHGAP11B,ANP32A-IT1,ADM5,BPIFA2,
C3,DGKH,GREM1,JPH1,KIAA1244,KIF14,MUC4,
MUC5B,NEUROG3,ODF2,PCSK9,SERPINA3,SNED1,SPTBN2
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 MUC5B


There's no related Drug.
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Cross referenced IDs for MUC5B
* 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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