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 MAN1B1
Basic gene info.Gene symbolMAN1B1
Gene namemannosidase, alpha, class 1B, member 1
SynonymsERMAN1|MANA-ER|MRT15
CytomapUCSC genome browser: 9q34
Genomic locationchr9 :139981378-140003639
Type of geneprotein-coding
RefGenesNM_016219.4,
NR_045720.1,NR_045721.1,
Ensembl idENSG00000177239
DescriptionER alpha 1,2-mannosidaseMan9GlcNAc2-specific processing alpha-mannosidaseendoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidaseendoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1
Modification date20141219
dbXrefs MIM : 604346
HGNC : HGNC
Ensembl : ENSG00000177239
HPRD : 05068
Vega : OTTHUMG00000020978
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MAN1B1
BioGPS: 11253
Gene Expression Atlas: ENSG00000177239
The Human Protein Atlas: ENSG00000177239
PathwayNCI Pathway Interaction Database: MAN1B1
KEGG: MAN1B1
REACTOME: MAN1B1
ConsensusPathDB
Pathway Commons: MAN1B1
MetabolismMetaCyc: MAN1B1
HUMANCyc: MAN1B1
RegulationEnsembl's Regulation: ENSG00000177239
miRBase: chr9 :139,981,378-140,003,639
TargetScan: NM_016219
cisRED: ENSG00000177239
ContextiHOP: MAN1B1
cancer metabolism search in PubMed: MAN1B1
UCL Cancer Institute: MAN1B1
Assigned class in ccmGDBC

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Phenotypic Information for MAN1B1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MAN1B1
Familial Cancer Database: MAN1B1
* 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: MAN1B1
MedGen: MAN1B1 (Human Medical Genetics with Condition)
ClinVar: MAN1B1
PhenotypeMGI: MAN1B1 (International Mouse Phenotyping Consortium)
PhenomicDB: MAN1B1

Mutations for MAN1B1
* 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
central_nervous_systemMAN1B1chr9139996694139996694MAN1B1chr9139997341139997341
ovaryMAN1B1chr9139994937139994957chr11277064612770666
pancreasMAN1B1chr9139996763139996783MAN1B1chr9139996529139996549
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 MAN1B1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF915326AMPD319251111049480510495037MAN1B12505419139981514139983346

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

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr9:140002989-140002989p.D682D4
chr9:139996024-139996024p.H385P2
chr9:139990753-139990753p.L177R2
chr9:139995548-139995548p.L339fs*22
chr9:140002938-140002938p.L665L2
chr9:139983453-139983453p.S154L2
chr9:140001201-140001201p.S502S2
chr9:140002995-140002995p.Y684Y2
chr9:139994260-139994260p.F281F2
chr9:140003024-140003024p.P694R2

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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
# sample42 5  2 1  512  58 3
# mutation52 5  2 1  512  59 5
nonsynonymous SNV52 2  1    4 1  46 5
synonymous SNV   3  1 1  111  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
chr9:139995979p.S17T1
chr9:139981500p.M298T1
chr9:140002104p.R629Q1
chr9:139990738p.M37V1
chr9:139995980p.D323Y1
chr9:139981560p.S635W1
chr9:140002847p.L87I1
chr9:139990814p.E330Q1
chr9:139996024p.I641I1
chr9:139982566p.L99L1

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 MAN1B1 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 MAN1B1

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

ANAPC2,C1orf122,PRADC1,C9orf142,C9orf69,RABL6,NELFB,
EDF1,FBXW5,JOSD2,LMAN2,MAN1B1,NTMT1,NDOR1,
PHPT1,PMPCA,PTGES2,REXO4,SDF4,SSNA1,SURF6
ARFGAP1,COQ4,CORO1B,DAK,DDX41,ERP29,GAK,
HMG20B,LRRC45,MAN1B1,NDOR1,NMRAL1,POMT1,PRKCSH,
RANGAP1,RUVBL2,SLC12A9,TRIM11,U2AF2,WDR46,YIPF2

ANAPC2,B3GAT3,C11orf68,C9orf142,NELFB,COQ4,DPP7,
EDF1,FBXW5,FPGS,LRSAM1,MAN1B1,MPG,NDOR1,
PHPT1,RNF208,SH3GLB2,SSNA1,SURF1,THAP3,TMEM203
B3GALT4,KDF1,DALRD3,DUSP23,ERGIC3,FCGRT,HMGCL,
HPS6,IMPA2,MAN1B1,C8orf82,PGLS,PXMP2,SLC35C2,
STAP2,TEX264,THAP4,TMEM134,ZDHHC12,ZDHHC24,ZNF524
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 MAN1B1
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
DB01955mannosidase, alpha, class 1B, member 1experimental1,4-Butanediol
DB02422mannosidase, alpha, class 1B, member 1experimentalMethyl-2-S-(Alpha-D-Mannopyranosyl)-2-Thio-Alpha-D-Mannopyranoside
DB02742mannosidase, alpha, class 1B, member 1experimentalKifunensine
DB02944mannosidase, alpha, class 1B, member 1experimentalAlpha-D-Mannose
DB03206mannosidase, alpha, class 1B, member 1experimental1-Deoxynojirimycin
DB00694mannosidase, alpha, class 1B, member 1approvedDaunorubicin


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Cross referenced IDs for MAN1B1
* 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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