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 LMAN1

Basic gene info.	Gene symbol	LMAN1
	Gene name	lectin, mannose-binding, 1
	Synonyms	ERGIC-53\|ERGIC53\|F5F8D\|FMFD1\|MCFD1\|MR60\|gp58
	Cytomap	UCSC genome browser: 18q21.3-q22
	Genomic location	chr18 :56995055-57026508
	Type of gene	protein-coding
	RefGenes	NM_005570.3,
	Ensembl id	ENSG00000074695
	Description	ER-Golgi intermediate compartment 53 kDa proteinendoplasmic reticulum-golgi intermediate compartment protein 53intracellular mannose specific lectinintracellular mannose-specific lectin MR60protein ERGIC-53
	Modification date	20141207
dbXrefs	MIM : 601567
	HGNC : HGNC
	Ensembl : ENSG00000074695
	HPRD : 03338
	Vega : OTTHUMG00000132758
Protein	UniProt: P49257 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LMAN1
	BioGPS: 3998
	Gene Expression Atlas: ENSG00000074695
	The Human Protein Atlas: ENSG00000074695
Pathway	NCI Pathway Interaction Database: LMAN1
	KEGG: LMAN1
	REACTOME: LMAN1
	ConsensusPathDB
	Pathway Commons: LMAN1
Metabolism	MetaCyc: LMAN1
	HUMANCyc: LMAN1
Regulation	Ensembl's Regulation: ENSG00000074695
	miRBase: chr18 :56,995,055-57,026,508
	TargetScan: NM_005570
	cisRED: ENSG00000074695
Context	iHOP: LMAN1
	cancer metabolism search in PubMed: LMAN1
	UCL Cancer Institute: LMAN1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for LMAN1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: LMAN1
	Familial Cancer Database: LMAN1

* 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 STAD ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	227300; phenotype. 227300; phenotype. 601567; gene. 601567; gene.
Orphanet	35909; Combined deficiency of factor V and factor VIII. 35909; Combined deficiency of factor V and factor VIII.
Disease	KEGG Disease: LMAN1
	MedGen: LMAN1 (Human Medical Genetics with Condition)
	ClinVar: LMAN1
Phenotype	MGI: LMAN1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: LMAN1

Mutations for LMAN1

* 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
ovary	LMAN1	chr18	57004391	57004411	CPLX4	chr18	56984492	56984512
ovary	LMAN1	chr18	57005845	57005865	LMAN1	chr18	57003213	57003233

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 LMAN1 related fusion information.

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

BU625653

LMAN1

599

56998744

57013282

KLF6

581

727

3819868

3820014

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=41)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=14)	Stat. for Insertions (# total SNVs=0)
	There's no inserted 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
chr18:57013194-57013194	p.E305fs*22	16
chr18:57022778-57022778	p.T109T	2
chr18:57013200-57013200	p.K302N	2
chr18:57014768-57014768	p.L267L	2
chr18:57021815-57021815	p.?	2
chr18:57022801-57022801	p.E102*	2
chr18:56998349-56998349	p.E503D	2
chr18:56998704-56998704	p.F481Y	1
chr18:57014755-57014755	p.G271E	1
chr18:57006031-57006031	p.I370I	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=1

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		1		4	2				2			5	2	1		1	6	4		6
# mutation		1		5	2				2			5	2	1		1	6	4		7
nonsynonymous SNV		1		4	1				1			5	2			1	6	1		7
synonymous SNV				1	1				1					1				3

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
chr18:57016437	p.C466R	1
chr18:56998729	p.L267L	1
chr18:57026271	p.E47Q	1
chr18:57013217	p.K465E	1
chr18:57016441	p.S261F	1
chr18:56998750	p.L16L	1
chr18:57026338	p.M458I	1
chr18:57013225	p.M236I	1
chr18:57020530	p.R456Q	1
chr18:56998753	p.D226Y	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 LMAN1 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 LMAN1

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


ADNP2,C18orf25,DYM,FECH,KDSR,KIAA1468,LMAN1, MEX3C,MIB1,NARS,PIAS2,PIGN,PIK3C3,ROCK1, RPRD1A,SMAD2,SMAD4,TMX3,TOR1AIP2,UGGT1,VPS4B	C5orf24,FNDC3A,G2E3,CFAP97,LMAN1,LMBR1,MIB1, MIER3,PPIP5K2,PRRC1,RLIM,SUZ12,TM9SF3,TMED7, TMEM106B,TMTC3,TRIM33,UBXN4,WDR36,ZBTB41,ZFYVE16

ASPH,TMEM263,TVP23B,FECH,HIF1A,HSP90B1,IER3IP1, KDSR,LMAN1,NARS,NUCB2,RTTN,SEC11C,SEC24D, SLC39A6,SMAD4,SOCS6,TMED10,TMX3,WDR7,ZNF24	CADPS2,CD44,CFH,DNAJC10,FNDC3A,GPR37,HIF1A, HRH2,HSP90B1,LMAN1,MCTP1,MORC4,NUCB2,PDIA5, RFX3,SEC24D,SLC10A7,SLC38A5,STT3A,USO1,XPO7

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 LMAN1

There's no related Drug.

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Cross referenced IDs for LMAN1

* 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