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 MAN1C1
Basic gene info.Gene symbolMAN1C1
Gene namemannosidase, alpha, class 1C, member 1
SynonymsHMIC|MAN1A3|MAN1C|pp6318
CytomapUCSC genome browser: 1p35
Genomic locationchr1 :25943958-26111258
Type of geneprotein-coding
RefGenesNM_001289010.1,
NM_020379.3,
Ensembl idENSG00000117643
Description1,2-alpha-mannosidase ICmannosyl-oligosaccharide 1,2-alpha-mannosidase ICprocessing alpha-1,2-mannosidase IC
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000117643
HPRD : 14354
Vega : OTTHUMG00000004417
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MAN1C1
BioGPS: 57134
Gene Expression Atlas: ENSG00000117643
The Human Protein Atlas: ENSG00000117643
PathwayNCI Pathway Interaction Database: MAN1C1
KEGG: MAN1C1
REACTOME: MAN1C1
ConsensusPathDB
Pathway Commons: MAN1C1
MetabolismMetaCyc: MAN1C1
HUMANCyc: MAN1C1
RegulationEnsembl's Regulation: ENSG00000117643
miRBase: chr1 :25,943,958-26,111,258
TargetScan: NM_001289010
cisRED: ENSG00000117643
ContextiHOP: MAN1C1
cancer metabolism search in PubMed: MAN1C1
UCL Cancer Institute: MAN1C1
Assigned class in ccmGDBC

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Phenotypic Information for MAN1C1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MAN1C1
Familial Cancer Database: MAN1C1
* 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: MAN1C1
MedGen: MAN1C1 (Human Medical Genetics with Condition)
ClinVar: MAN1C1
PhenotypeMGI: MAN1C1 (International Mouse Phenotyping Consortium)
PhenomicDB: MAN1C1

Mutations for MAN1C1
* 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
breastMAN1C1chr12608166826081668SCMH1chr14157995041579950
central_nervous_systemMAN1C1chr12609432926094329MAN1C1chr12609484326094843
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 MAN1C1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI036406MAN1C11412312603433326034445THTPA119323142402631524026519
AF318353RNF1451710465158623238158624266MAN1C11047367612594434126110941

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 # sample1                
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr1:25944741-25944741p.R151R3
chr1:26104703-26104703p.S455S2
chr1:26098221-26098221p.K405K2
chr1:26104716-26104716p.A460T2
chr1:26012982-26012982p.E198K2
chr1:26104797-26104797p.E487K2
chr1:26012988-26012988p.R200C2
chr1:26104628-26104628p.P430P2
chr1:25944326-25944326p.S13F1
chr1:26075787-26075787p.I265I1

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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
# sample3  11  3    24   87 7
# mutation3  12  4    24   127 7
nonsynonymous SNV3  10  2    23   72 6
synonymous SNV   2  2     1   55 1
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
chr1:26012982p.E198K,MAN1C12
chr1:26012988p.R200C,MAN1C12
chr1:25944326p.S13F,MAN1C11
chr1:26104703p.Y207Y,MAN1C11
chr1:26012975p.S455S,MAN1C11
chr1:26109126p.T610T1
chr1:26085168p.L26P,MAN1C11
chr1:25944365p.T226T,MAN1C11
chr1:26104704p.G456R,MAN1C11
chr1:26012981p.D621N1

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 MAN1C1 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 MAN1C1

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

ADD1,ARHGAP6,CBX7,CLCN6,CRY2,ECE1,FUCA1,
LDLRAP1,MAGED2,MAN1C1,PDE2A,PGPEP1,JADE2,SEPN1,
SETBP1,SLC9A1,SYTL2,TADA2B,TMEM63C,TRIM62,ZFYVE28
C1QTNF2,C1S,C3,CCDC80,CD34,FBLN1,FBLN5,
GDF10,GPR133,LHFP,LRRN4CL,MAN1C1,MFAP4,OLFML1,
CPQ,PODN,PRRX1,PTGIS,SERPING1,TIMP2,TPST1

A2M,BOC,CACNA2D1,CLIP4,COL14A1,FBLN5,FLRT2,
ITPR1,JAM2,LRRN4CL,MAN1C1,MAPK10,MOXD1,PGR,
RBMS3,RNF150,RUNX1T1,SETBP1,SLC8A1,SLC9A9,ZEB1
ABCB5,CHST14,COL6A3,DCLK1,FKBP10,GPR124,GPRC5B,
HHIPL1,LRRC2,MAN1C1,MXRA8,MYH10,NRP1,OLFML1,
PODN,PTPRS,RPS6KA2,SERPING1,THBS2,VIM,ZNF521
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 MAN1C1


There's no related Drug.
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Cross referenced IDs for MAN1C1
* 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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