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 MAN2A1
Basic gene info.Gene symbolMAN2A1
Gene namemannosidase, alpha, class 2A, member 1
SynonymsAMan II|GOLIM7|MANA2|MANII
CytomapUCSC genome browser: 5q21.3
Genomic locationchr5 :109025155-109203429
Type of geneprotein-coding
RefGenesNM_002372.3,
Ensembl idENSG00000112893
DescriptionGolgi alpha-mannosidase IIalpha-mannosidase 2golgi integral membrane protein 7mannosidase, alpha type IImannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
Modification date20141207
dbXrefs MIM : 154582
HGNC : HGNC
HPRD : 01110
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MAN2A1
BioGPS: 4124
Gene Expression Atlas: ENSG00000112893
The Human Protein Atlas: ENSG00000112893
PathwayNCI Pathway Interaction Database: MAN2A1
KEGG: MAN2A1
REACTOME: MAN2A1
ConsensusPathDB
Pathway Commons: MAN2A1
MetabolismMetaCyc: MAN2A1
HUMANCyc: MAN2A1
RegulationEnsembl's Regulation: ENSG00000112893
miRBase: chr5 :109,025,155-109,203,429
TargetScan: NM_002372
cisRED: ENSG00000112893
ContextiHOP: MAN2A1
cancer metabolism search in PubMed: MAN2A1
UCL Cancer Institute: MAN2A1
Assigned class in ccmGDBC

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Phenotypic Information for MAN2A1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MAN2A1
Familial Cancer Database: MAN2A1
* 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: MAN2A1
MedGen: MAN2A1 (Human Medical Genetics with Condition)
ClinVar: MAN2A1
PhenotypeMGI: MAN2A1 (International Mouse Phenotyping Consortium)
PhenomicDB: MAN2A1

Mutations for MAN2A1
* 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
ovaryMAN2A1chr5109055821109055841MAN2A1chr5109066795109066815
ovaryMAN2A1chr5109124750109124770MAN2A1chr5109124865109124885
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 MAN2A1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI474018MAN2A11735109194057109194129KCNH87140731939037319390709

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 # sample      2        1 
GAIN (# sample)               1 
LOSS (# sample)      2          
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=99)
Stat. for Synonymous SNVs
(# total SNVs=30)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=1)

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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
chr5:109124646-109124646p.S591L3
chr5:109110611-109110611p.K440R3
chr5:109155490-109155490p.G744R3
chr5:109120589-109120589p.G574G3
chr5:109120470-109120470p.A535T3
chr5:109155562-109155562p.R768W3
chr5:109183456-109183456p.R981*3
chr5:109120509-109120509p.L548I2
chr5:109155379-109155379p.R707*2
chr5:109190857-109190857p.S998L2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample55 16  3 3  1763  75 19
# mutation55 16  3 3  2063  116 25
nonsynonymous SNV53 14  2 3  1652  85 16
synonymous SNV 2 2  1    411  31 9
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
chr5:109155562p.R768W3
chr5:109120589p.G574G3
chr5:109152986p.I641M2
chr5:109110522p.V652V2
chr5:109120509p.S662L2
chr5:109153015p.S998L2
chr5:109190857p.L548I2
chr5:109125208p.K410N2
chr5:109191017p.L471L1
chr5:109026131p.L809I1

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 MAN2A1 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 MAN2A1

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

AFF4,APC,CCNT1,FER,GTF2A1,HMBOX1,LMBRD2,
LNPEP,MAN2A1,MFAP3,NBEAL1,PJA2,POLK,RAPGEF6,
REL,SCAF11,SLC25A46,TCP11L2,TTC37,UHMK1,UHRF1BP1L
CAMSAP2,DENND4A,DNAJB14,DNAJC13,HIPK1,ITCH,ITGAV,
MAN2A1,MAP3K2,MOB1A,PIK3C2A,SETX,SLC30A6,SLK,
STRN,TBCEL,TMOD3,TRIM44,VPS13C,WDFY3,XRN1

AFF4,ASXL2,CCNT1,DDI2,DMXL1,GTF2A1,HIPK3,
LMBRD2,LNPEP,MAN1A2,MAN2A1,PRKAR2A,PTPLB,RAPGEF6,
RC3H2,REL,REST,SCYL2,SERINC5,TAOK1,UHMK1
ADAM10,AP1G1,ARFGEF1,ARHGAP32,PRR14L,CNOT1,CPD,
DSP,ITPR3,AREL1,LRRC16A,MAN2A1,MARCH6,MFSD9,
MYO5B,OSBP,PTPLB,PTPRK,RREB1,TMPPE,UBE4A
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 MAN2A1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02034mannosidase, alpha, class 2A, member 1experimentalSwainsonine
DB02318mannosidase, alpha, class 2A, member 1experimental2-Deoxy-2-Fluoro-Alpha-D-Mannosyl Fluoride
DB02492mannosidase, alpha, class 2A, member 1experimentalGhavamiol
DB02742mannosidase, alpha, class 2A, member 1experimentalKifunensine
DB03008mannosidase, alpha, class 2A, member 1experimental5-Fluoro-Beta-L-Gulosyl Fluoride
DB03414mannosidase, alpha, class 2A, member 1experimental5-Thio-a/B-D-Mannopyranosylamine
DB03955mannosidase, alpha, class 2A, member 1experimental1,5-Dideoxy-1,5-Imino-D-Mannitol
DB06984mannosidase, alpha, class 2A, member 1experimental(1R,2R,3R,4S,5R)-4-(BENZYLAMINO)-5-(METHYLTHIO)CYCLOPENTANE-1,2,3-TRIOL
DB08321mannosidase, alpha, class 2A, member 1experimental(1S,2S,3R,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol


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Cross referenced IDs for MAN2A1
* 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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