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 MAN1A2

Basic gene info.	Gene symbol	MAN1A2
	Gene name	mannosidase, alpha, class 1A, member 2
	Synonyms	MAN1B
	Cytomap	UCSC genome browser: 1p13
	Genomic location	chr1 :117910084-118068320
	Type of gene	protein-coding
	RefGenes	NM_006699.3,
	Ensembl id	ENSG00000198162
	Description	alpha-1,2-mannosidase IBalpha1,2-mannosidasemannosyl-oligosaccharide 1,2-alpha-mannosidase IBprocessing alpha-1,2-mannosidase IB
	Modification date	20141207
dbXrefs	MIM : 604345
	HGNC : HGNC
	Ensembl : ENSG00000198162
	HPRD : 05067
	Vega : OTTHUMG00000012149
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MAN1A2
	BioGPS: 10905
	Gene Expression Atlas: ENSG00000198162
	The Human Protein Atlas: ENSG00000198162
Pathway	NCI Pathway Interaction Database: MAN1A2
	KEGG: MAN1A2
	REACTOME: MAN1A2
	ConsensusPathDB
	Pathway Commons: MAN1A2
Metabolism	MetaCyc: MAN1A2
	HUMANCyc: MAN1A2
Regulation	Ensembl's Regulation: ENSG00000198162
	miRBase: chr1 :117,910,084-118,068,320
	TargetScan: NM_006699
	cisRED: ENSG00000198162
Context	iHOP: MAN1A2
	cancer metabolism search in PubMed: MAN1A2
	UCL Cancer Institute: MAN1A2
Assigned class in ccmGDB	C

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Phenotypic Information for MAN1A2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MAN1A2
	Familial Cancer Database: MAN1A2

* 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: MAN1A2
	MedGen: MAN1A2 (Human Medical Genetics with Condition)
	ClinVar: MAN1A2
Phenotype	MGI: MAN1A2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MAN1A2

Mutations for MAN1A2

* 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
ovary	MAN1A2	chr1	117937101	117937121	MAN1A2	chr1	117957567	117957587
ovary	MAN1A2	chr1	118034766	118034786	MAN1A2	chr1	118023660	118023680
ovary	MAN1A2	chr1	118062491	118062511	MAN1A2	chr1	118011584	118011604
ovary	MAN1A2	chr1	118066481	118066501	XXYLT1	chr3	194883928	194883948
pancreas	MAN1A2	chr1	118016991	118017011	MAN1A2	chr1	118017044	118017064
pancreas	MAN1A2	chr1	118041255	118041275	MAN1A2	chr1	118043647	118043667

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 MAN1A2 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
AW801968	MAN1A2	1	126	1	117944806	117944931	MAN1A2	124	200	1	117963196	117963272
AA668350	MAN1A2	1	206	1	117944806	117945011	MAN1A2	204	410	1	117957327	117963272
AK023308	MAN1A2	1	1417	1	117910565	118042028	KIAA2018	1412	2371	3	113374275	113375234
AA730065	MAN1A2	36	426	1	117944971	117963272	GYPC	416	435	2	127452947	127452966
AI768882	MAN1A2	1	58	1	117944806	117944863	MAN1A2	56	242	1	117957349	117963272
BE832742	MAN1A2	1	227	1	117948242	117963272	MAN1A2	225	289	1	117944806	117945074
BF354622	DST	30	154	6	56329531	56329656	MAN1A2	146	352	1	117950895	117951099
BG000012	EML2	8	193	19	46128976	46129161	MAN1A2	182	400	1	117986828	117987045
AA368655	MAN1A2	1	99	1	117910980	117911078	ZYX	98	296	7	143087669	143087867
BU859918	MAN1A2	28	50	1	117953465	117953492	LONP1	34	792	19	5691845	5693781
BE832754	MAN1A2	26	226	1	117957334	117963272	MAN1A2	224	288	1	117944806	117945074
BC004934	LONP1	1	1752	19	5691845	5705823	MAN1A2	1736	1758	1	117953465	117953492
DW434893	MAN1A2	17	104	1	117957367	117957454	MAN1A2	103	206	1	117944807	117944910
AW894933	MAN1A2	4	186	1	117944806	117944987	MAN1A2	184	366	1	117957353	117963272

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	3			2					2		4		1	1	2		1
GAIN (# sample)	3			2					1		4		1	1	2		1
LOSS (# sample)									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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=38)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr1:117944839-117944839	p.R112*	3
chr1:117984892-117984892	p.L299F	3
chr1:117910917-117910917	p.I38V	2
chr1:117944905-117944905	p.R134*	2
chr1:118042153-118042153	p.Q552*	2
chr1:117944919-117944919	p.Q138Q	2
chr1:117944941-117944941	p.Q146*	2
chr1:117984948-117984948	p.?	2
chr1:117944820-117944820	p.E105E	1
chr1:118035780-118035780	p.V394F	1

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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=2

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	4	3	1	8			1					10	4	2			3	6		5
# mutation	4	3	1	8			1					13	4	2			2	6		5
nonsynonymous SNV	2		1	4								10	4				1	3		5
synonymous SNV	2	3		4			1					3		2			1	3

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
chr1:117984892	p.Q138Q	2
chr1:117944919	p.L299F	2
chr1:117944840	p.L9L	1
chr1:118042173	p.S438Y	1
chr1:117948265	p.L19L	1
chr1:117910832	p.P160R	1
chr1:118039413	p.G451G	1
chr1:117944862	p.G20G	1
chr1:118045525	p.I161V	1
chr1:117957422	p.H452H	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 MAN1A2 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 MAN1A2

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


ASXL2,ATP1A1,BIRC6,CD58,CLOCK,CTNND1,GDAP2, IGSF3,KCTD14,MAN1A2,MAP3K2,NBEAL1,NOTCH2,OR6Q1, PTGFRN,REST,SEC22B,SLC43A3,TOR1AIP2,VTCN1,WDR3	ANKIB1,ARHGAP42,ATL3,CDC42BPA,CLOCK,EXOC6B,FER, FNDC3B,HEATR5A,LNPEP,MAN1A2,MBNL3,PBRM1,RC3H2, SBF2,TAOK1,TRIM44,TRIP12,USP12,UTRN,XPOT

ANKRD36BP1,ASXL2,DDI2,FAM168A,FAM63B,FAM73A,GTF2A1, HIPK1,HIPK3,IL6ST,MAN1A2,MAP3K2,MYO9A,NOTCH2, RC3H2,REST,RSC1A1,TAOK1,TRIM33,UHMK1,ZNF106	SOGA1,CLOCK,FAM63B,HIPK3,IL6ST,KIAA0754,ICE1, KIRREL,LATS1,LNPEP,MAN1A2,NAA25,PBRM1,PIK3C2A, PTPN11,PTPRG,ROCK1,TAOK1,TRAF3IP1,TRIM44,ZC3H13

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 MAN1A2

There's no related Drug.

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Cross referenced IDs for MAN1A2

* 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