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 MAN1A1

Basic gene info.	Gene symbol	MAN1A1
	Gene name	mannosidase, alpha, class 1A, member 1
	Synonyms	HUMM3\|HUMM9\|MAN9
	Cytomap	UCSC genome browser: 6q22
	Genomic location	chr6 :119499266-119670926
	Type of gene	protein-coding
	RefGenes	NM_005907.3,
	Ensembl id	ENSG00000111885
	Description	Man9-mannosidasealpha-1,2-mannosidase IAman(9)-alpha-mannosidasemannosyl-oligosaccharide 1,2-alpha-mannosidase IAprocessing alpha-1,2-mannosidase IA
	Modification date	20141207
dbXrefs	MIM : 604344
	HGNC : HGNC
	Ensembl : ENSG00000111885
	HPRD : 05066
	Vega : OTTHUMG00000015472
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MAN1A1
	BioGPS: 4121
	Gene Expression Atlas: ENSG00000111885
	The Human Protein Atlas: ENSG00000111885
Pathway	NCI Pathway Interaction Database: MAN1A1
	KEGG: MAN1A1
	REACTOME: MAN1A1
	ConsensusPathDB
	Pathway Commons: MAN1A1
Metabolism	MetaCyc: MAN1A1
	HUMANCyc: MAN1A1
Regulation	Ensembl's Regulation: ENSG00000111885
	miRBase: chr6 :119,499,266-119,670,926
	TargetScan: NM_005907
	cisRED: ENSG00000111885
Context	iHOP: MAN1A1
	cancer metabolism search in PubMed: MAN1A1
	UCL Cancer Institute: MAN1A1
Assigned class in ccmGDB	C

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Phenotypic Information for MAN1A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MAN1A1
	Familial Cancer Database: MAN1A1

* 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
Orphanet
Disease	KEGG Disease: MAN1A1
	MedGen: MAN1A1 (Human Medical Genetics with Condition)
	ClinVar: MAN1A1
Phenotype	MGI: MAN1A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MAN1A1

Mutations for MAN1A1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	MAN1A1	chr6	119558570	119558663		chr6	82754655	82754768
NS	MAN1A1	chr6	119558561	119558561	PID1	chr2	230045479	230045479
NS	MAN1A1	chr6	119558562	119558562	HFM1	chr1	91852808	91852808
ovary	MAN1A1	chr6	119505609	119505629		chr2	127732135	127732155
ovary	MAN1A1	chr6	119561062	119561082	CEP85L	chr6	118851106	118851126
ovary	MAN1A1	chr6	119653779	119653799	MAN1A1	chr6	119654439	119654459

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 MAN1A1 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
AA828041	MAN1A1	4	376	6	119500279	119500651	MAN1A1	369	428	6	119500228	119500287
X74837	TEK	1	750	9	27160653	27161403	MAN1A1	747	3232	6	119500317	119670089

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	1							2		2		2		1		1
GAIN (# sample)	2	1							2				1
LOSS (# sample)											2		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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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=53)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr6:119569512-119569512	p.R302Q	4
chr6:119510873-119510873	p.G501E	2
chr6:119623172-119623172	p.E266G	2
chr6:119509656-119509656	p.R545W	2
chr6:119510998-119510998	p.I459I	2
chr6:119511012-119511012	p.G455R	2
chr6:119510902-119510902	p.E491E	2
chr6:119501033-119501033	p.L638P	2
chr6:119510834-119510834	p.R514Q	2
chr6:119669822-119669822	p.E137K	2

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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=3

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	2	2		13	2		1		1			3	4	2		3	12	2		11
# mutation	2	2		13	2		1		1			3	4	2		3	13	2		14
nonsynonymous SNV	2	1		12	1				1			1	4	2		2	12	1		12
synonymous SNV		1		1	1		1					2				1	1	1		2

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
chr6:119509656	p.R545W	2
chr6:119510998	p.G501E	2
chr6:119511012	p.L638P	2
chr6:119501033	p.S633S	2
chr6:119501047	p.R302Q	2
chr6:119510873	p.I459I	2
chr6:119569512	p.G455R	2
chr6:119522442	p.E445K	1
chr6:119670168	p.E259Q	1
chr6:119623164	p.A58T	1

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 MAN1A1 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 MAN1A1

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


LINC00589,CPEB4,ENPP1,FAM65C,FAM73A,MAP10,KRT40, KRTAP1-3,KRTAP1-5,KRTAP3-2,KRTAP3-3,MAN1A1,MBOAT2,NPY6R, PARP8,PDZRN3,PRLR,SIPA1L2,SPAG17,WDFY3,ZNRF3	ARHGAP21,CDKN2B,CELF2,CHRDL1,DSE,ECM2,EPB41L2, EPS8,GNS,ITGB1,LAMC1,MAN1A1,NEK7,OSTM1, PARVA,SEPT11,SESTD1,SH3D19,TACC1,VGLL3,ZEB2

ABCA1,ARSB,BMP2K,CD93,CPEB4,EPAS1,IL6ST, KDR,LILRA1,LRRC8C,MAN1A1,N4BP2,PLEKHG1,PLXNC1, SASH1,SECISBP2L,PEAK1,SLC30A4,TRAM2,UTRN,ZNF366	ABAT,BMF,NCMAP,EPB41L3,HADHA,HADHB,IL13RA1, IPMK,KBTBD11,LAMP2,LPCAT3,MAN1A1,MARCH8,PBLD, SCAMP5,SNX24,TMEM19,TNIK,TOR1AIP2,UBTD2,VPS35

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 MAN1A1

There's no related Drug.

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Cross referenced IDs for MAN1A1

* 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