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 MAN1A2
Basic gene info.Gene symbolMAN1A2
Gene namemannosidase, alpha, class 1A, member 2
SynonymsMAN1B
CytomapUCSC genome browser: 1p13
Genomic locationchr1 :117910084-118068320
Type of geneprotein-coding
RefGenesNM_006699.3,
Ensembl idENSG00000198162
Descriptionalpha-1,2-mannosidase IBalpha1,2-mannosidasemannosyl-oligosaccharide 1,2-alpha-mannosidase IBprocessing alpha-1,2-mannosidase IB
Modification date20141207
dbXrefs MIM : 604345
HGNC : HGNC
Ensembl : ENSG00000198162
HPRD : 05067
Vega : OTTHUMG00000012149
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MAN1A2
BioGPS: 10905
Gene Expression Atlas: ENSG00000198162
The Human Protein Atlas: ENSG00000198162
PathwayNCI Pathway Interaction Database: MAN1A2
KEGG: MAN1A2
REACTOME: MAN1A2
ConsensusPathDB
Pathway Commons: MAN1A2
MetabolismMetaCyc: MAN1A2
HUMANCyc: MAN1A2
RegulationEnsembl's Regulation: ENSG00000198162
miRBase: chr1 :117,910,084-118,068,320
TargetScan: NM_006699
cisRED: ENSG00000198162
ContextiHOP: MAN1A2
cancer metabolism search in PubMed: MAN1A2
UCL Cancer Institute: MAN1A2
Assigned class in ccmGDBC

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Phenotypic Information for MAN1A2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MAN1A2
MedGen: MAN1A2 (Human Medical Genetics with Condition)
ClinVar: MAN1A2
PhenotypeMGI: MAN1A2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryMAN1A2chr1117937101117937121MAN1A2chr1117957567117957587
ovaryMAN1A2chr1118034766118034786MAN1A2chr1118023660118023680
ovaryMAN1A2chr1118062491118062511MAN1A2chr1118011584118011604
ovaryMAN1A2chr1118066481118066501XXYLT1chr3194883928194883948
pancreasMAN1A2chr1118016991118017011MAN1A2chr1118017044118017064
pancreasMAN1A2chr1118041255118041275MAN1A2chr1118043647118043667
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 MAN1A2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW801968MAN1A211261117944806117944931MAN1A21242001117963196117963272
AA668350MAN1A212061117944806117945011MAN1A22044101117957327117963272
AK023308MAN1A2114171117910565118042028KIAA2018141223713113374275113375234
AA730065MAN1A2364261117944971117963272GYPC4164352127452947127452966
AI768882MAN1A21581117944806117944863MAN1A2562421117957349117963272
BE832742MAN1A212271117948242117963272MAN1A22252891117944806117945074
BF354622DST3015465632953156329656MAN1A21463521117950895117951099
BG000012EML28193194612897646129161MAN1A21824001117986828117987045
AA368655MAN1A21991117910980117911078ZYX982967143087669143087867
BU859918MAN1A228501117953465117953492LONP1347921956918455693781
BE832754MAN1A2262261117957334117963272MAN1A22242881117944806117945074
BC004934LONP1117521956918455705823MAN1A2173617581117953465117953492
DW434893MAN1A2171041117957367117957454MAN1A21032061117944807117944910
AW894933MAN1A241861117944806117944987MAN1A21843661117957353117963272

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 # sample3  2    2 4 112 1
GAIN (# sample)3  2    1 4 112 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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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=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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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
chr1:117944839-117944839p.R112*3
chr1:117984892-117984892p.L299F3
chr1:117910917-117910917p.I38V2
chr1:117944905-117944905p.R134*2
chr1:118042153-118042153p.Q552*2
chr1:117944919-117944919p.Q138Q2
chr1:117944941-117944941p.Q146*2
chr1:117984948-117984948p.?2
chr1:117944820-117944820p.E105E1
chr1:118035780-118035780p.V394F1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample4318  1    1042  36 5
# mutation4318  1    1342  26 5
nonsynonymous SNV2 14       104   13 5
synonymous SNV23 4  1    3 2  13  
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
chr1:117984892p.Q138Q2
chr1:117944919p.L299F2
chr1:117944840p.L9L1
chr1:118042173p.S438Y1
chr1:117948265p.L19L1
chr1:117910832p.P160R1
chr1:118039413p.G451G1
chr1:117944862p.G20G1
chr1:118045525p.I161V1
chr1:117957422p.H452H1

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 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

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

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
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 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



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