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 MAN1C1

Basic gene info.	Gene symbol	MAN1C1
	Gene name	mannosidase, alpha, class 1C, member 1
	Synonyms	HMIC\|MAN1A3\|MAN1C\|pp6318
	Cytomap	UCSC genome browser: 1p35
	Genomic location	chr1 :25943958-26111258
	Type of gene	protein-coding
	RefGenes	NM_001289010.1, NM_020379.3,
	Ensembl id	ENSG00000117643
	Description	1,2-alpha-mannosidase ICmannosyl-oligosaccharide 1,2-alpha-mannosidase ICprocessing alpha-1,2-mannosidase IC
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000117643
	HPRD : 14354
	Vega : OTTHUMG00000004417
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MAN1C1
	BioGPS: 57134
	Gene Expression Atlas: ENSG00000117643
	The Human Protein Atlas: ENSG00000117643
Pathway	NCI Pathway Interaction Database: MAN1C1
	KEGG: MAN1C1
	REACTOME: MAN1C1
	ConsensusPathDB
	Pathway Commons: MAN1C1
Metabolism	MetaCyc: MAN1C1
	HUMANCyc: MAN1C1
Regulation	Ensembl's Regulation: ENSG00000117643
	miRBase: chr1 :25,943,958-26,111,258
	TargetScan: NM_001289010
	cisRED: ENSG00000117643
Context	iHOP: MAN1C1
	cancer metabolism search in PubMed: MAN1C1
	UCL Cancer Institute: MAN1C1
Assigned class in ccmGDB	C

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Phenotypic Information for MAN1C1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MAN1C1
	MedGen: MAN1C1 (Human Medical Genetics with Condition)
	ClinVar: MAN1C1
Phenotype	MGI: MAN1C1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	MAN1C1	chr1	26081668	26081668	SCMH1	chr1	41579950	41579950
central_nervous_system	MAN1C1	chr1	26094329	26094329	MAN1C1	chr1	26094843	26094843

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 MAN1C1 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
BI036406	MAN1C1	14	123	1	26034333	26034445	THTPA	119	323	14	24026315	24026519
AF318353	RNF145	17	1046	5	158623238	158624266	MAN1C1	1047	3676	1	25944341	26110941

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=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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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
chr1:25944741-25944741	p.R151R	3
chr1:26104703-26104703	p.S455S	2
chr1:26098221-26098221	p.K405K	2
chr1:26104716-26104716	p.A460T	2
chr1:26012982-26012982	p.E198K	2
chr1:26104797-26104797	p.E487K	2
chr1:26012988-26012988	p.R200C	2
chr1:26104628-26104628	p.P430P	2
chr1:26013026-26013026	p.F212F	1
chr1:26104700-26104700	p.F454F	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	3			11			3					2	4				8	7		7
# mutation	3			12			4					2	4				12	7		7
nonsynonymous SNV	3			10			2					2	3				7	2		6
synonymous SNV				2			2						1				5	5		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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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
chr1:26012982	p.E198K,MAN1C1	2
chr1:26012988	p.R200C,MAN1C1	2
chr1:26085168	p.N197N,MAN1C1	1
chr1:26104704	p.G431G,MAN1C1	1
chr1:25944365	p.V568M,MAN1C1	1
chr1:26012981	p.A437A,MAN1C1	1
chr1:26109127	p.E586D,MAN1C1	1
chr1:26090398	p.E438K,MAN1C1	1
chr1:26104708	p.L591L	1
chr1:25944443	p.G206D,MAN1C1	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 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

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


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

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 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