Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	MUC5B
	Gene name	mucin 5B, oligomeric mucus/gel-forming
	Synonyms	MG1\|MUC-5B\|MUC5\|MUC9
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :1244294-1283406
	Type of gene	protein-coding
	RefGenes	NM_002458.2,
	Ensembl id	ENSG00000117983
	Description	cervical mucin MUC5Bhigh molecular weight salivary mucin MG1mucin 5, subtype B, tracheobronchialmucin-5Bsublingual gland mucin
	Modification date	20141222
dbXrefs	MIM : 600770
	HGNC : HGNC
	Ensembl : ENSG00000117983
	Vega : OTTHUMG00000166494
Protein	UniProt: Q9HC84 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MUC5B
	BioGPS: 727897
	Gene Expression Atlas: ENSG00000117983
	The Human Protein Atlas: ENSG00000117983
Pathway	NCI Pathway Interaction Database: MUC5B
	KEGG: MUC5B
	REACTOME: MUC5B
	ConsensusPathDB
	Pathway Commons: MUC5B
Metabolism	MetaCyc: MUC5B
	HUMANCyc: MUC5B
Regulation	Ensembl's Regulation: ENSG00000117983
	miRBase: chr11 :1,244,294-1,283,406
	TargetScan: NM_002458
	cisRED: ENSG00000117983
Context	iHOP: MUC5B
	cancer metabolism search in PubMed: MUC5B
	UCL Cancer Institute: MUC5B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for MUC5B(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	178500; phenotype. 178500; phenotype. 600770; gene. 600770; gene.
Orphanet	171700; Diffuse panbronchiolitis. 171700; Diffuse panbronchiolitis. 2032; Idiopathic pulmonary fibrosis. 2032; Idiopathic pulmonary fibrosis.
Disease	KEGG Disease: MUC5B
	MedGen: MUC5B (Human Medical Genetics with Condition)
	ClinVar: MUC5B
Phenotype	MGI: MUC5B (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	MUC5B	chr11	1258980	1259380	CARS	chr11	3052157	3052557

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MUC5B related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG955818	MUC5B	11	210	11	1271330	1271533	MLEC	202	403	12	121139214	121139415
BQ320008	GHITM	25	123	10	85902474	85903812	MUC5B	124	338	11	1263615	1263829

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr11:1253969-1253969	p.V678V	11
chr11:1253976-1253976	p.S681G	7
chr11:1258286-1258286	p.D1063D	7
chr11:1258283-1258283	p.P1062P	6
chr11:1263216-1263216	p.T1702T	5
chr11:1268931-1268931	p.A3607A	5
chr11:1271321-1271321	p.A4404G	4
chr11:1261118-1261118	p.G1225R	4
chr11:1253980-1253980	p.D682G	4
chr11:1267325-1267325	p.F3072S	4

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	7	33	2	43	10		24	1	11	3	3	47	33	5	1	2	45	38	6	57
# mutation	7	35	2	54	12		27	1	11	3	4	60	41	5	1	2	66	61	6	106
nonsynonymous SNV	5	19	2	30	6		20	1	9	3	3	40	31	4		2	45	34	4	71
synonymous SNV	2	16		24	6		7		2		1	20	10	1	1		21	27	2	35

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr11:1261118	p.G1225R	4
chr11:1265872	p.G2588R	3
chr11:1265445	p.A3700T	2
chr11:1267649	p.T3115T	2
chr11:1271501	p.S681G	2
chr11:1264225	p.T3131T	2
chr11:1253976	p.P5635T	2
chr11:1270908	p.D682G	2
chr11:1253980	p.G4464E	2
chr11:1265999	p.E2315K	2

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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