Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 LGMN

Basic gene info.	Gene symbol	LGMN
	Gene name	legumain
	Synonyms	AEP\|LGMN1\|PRSC1
	Cytomap	UCSC genome browser: 14q32.1
	Genomic location	chr14 :93170151-93215047
	Type of gene	protein-coding
	RefGenes	NM_001008530.2, NM_005606.6,
	Ensembl id	ENSG00000100600
	Description	asparaginyl endopeptidasecysteine protease 1protease, cysteine 1protease, cysteine, 1 (legumain)
	Modification date	20141207
dbXrefs	MIM : 602620
	HGNC : HGNC
	Ensembl : ENSG00000100600
	HPRD : 04017
	Vega : OTTHUMG00000171199
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LGMN
	BioGPS: 5641
	Gene Expression Atlas: ENSG00000100600
	The Human Protein Atlas: ENSG00000100600
Pathway	NCI Pathway Interaction Database: LGMN
	KEGG: LGMN
	REACTOME: LGMN
	ConsensusPathDB
	Pathway Commons: LGMN
Metabolism	MetaCyc: LGMN
	HUMANCyc: LGMN
Regulation	Ensembl's Regulation: ENSG00000100600
	miRBase: chr14 :93,170,151-93,215,047
	TargetScan: NM_001008530
	cisRED: ENSG00000100600
Context	iHOP: LGMN
	cancer metabolism search in PubMed: LGMN
	UCL Cancer Institute: LGMN
Assigned class in ccmGDB	C

Top

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

Cancer Description
Cancer	CGAP: LGMN
	Familial Cancer Database: LGMN

* 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_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for LGMN

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LGMN 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
CN269392	RPL18	7	510	19	49119141	49122421	LGMN	502	618	14	93170154	93170270
AU138144	LOC100507412	1	122	?	109636	109757	LGMN	123	661	14	93182516	93214972
AW450755	COL6A3	18	100	2	238232660	238232742	LGMN	97	368	14	93178236	93180796
AA157183	LGMN	1	85	14	93214868	93214953	ENO1	86	422	1	8928060	8938673
BP392190	LGMN	1	113	14	93176154	93178052	VCAN	113	501	5	82876748	82877136
AW753026	LGMN	100	261	14	93183766	93185212	LGMN	256	482	14	93182289	93182515
BC008004	VPS4A	30	998	16	69356476	69358908	LGMN	999	2936	14	93170154	93214930

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=21)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr14:93185098-93185098	p.S77F	3
chr14:93170993-93170993	p.P417P	3
chr14:93178266-93178266	p.S215S	2
chr14:93199080-93199080	p.V18I	2
chr14:93182544-93182544	p.L114R	2
chr14:93179217-93179217	p.?	2
chr14:93180173-93180173	p.R180R	2
chr14:93172829-93172829	p.T397M	1
chr14:93180774-93180774	p.I143V	1
chr14:93176079-93176079	p.M320V	1

Top

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

Top

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
chr14:93178266	p.L339L,LGMN	2
chr14:93185138	p.E64K,LGMN	2
chr14:93176022	p.S215S,LGMN	2
chr14:93172867	p.L198M,LGMN	1
chr14:93178208	p.L402L,LGMN	1
chr14:93183739	p.Y179Y,LGMN	1
chr14:93172963	p.T397M,LGMN	1
chr14:93183754	p.I143S,LGMN	1
chr14:93172970	p.L384L,LGMN	1
chr14:93178281	p.I143V,LGMN	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 LGMN 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]

Top

Gene Expression for LGMN

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ADAP2,CD163,CD300A,CD68,CD86,CTSL,EMILIN2, FPR3,HAVCR2,IFI30,LAIR1,LGMN,LILRB3,MS4A4A, PILRA,PLEKHO2,SIGLEC1,SIGLEC7,SIGLEC9,SLC7A7,TMEM150B	BCAT1,C2,C3AR1,CD33,CLEC10A,CMKLR1,CSF1R, FOLR2,HAVCR2,ITGAM,LGMN,LILRA6,LILRB5,MPP1, MS4A4A,MS4A6A,NCF2,RASGRP4,RNASE1,SIGLEC1,VSIG4

APOBEC3G,APOL3,C1QC,CCL5,CTSW,GBP1,GBP2, GBP4,IFI30,IFIT3,IL18BP,LAP3,LGMN,LOC400759, PIK3AP1,SLC15A3,STAT1,STAT2,TNFSF13B,UBE2L6,WARS	ACRBP,ALDH3B1,ARRB2,CD68,DNASE1L1,EMB,FTL, GHDC,KCNG2,LGMN,LIPA,LOC647121,MST1,PFKFB4, RHBDL1,SEC16B,SERPINA1,SIRPA,SLC2A7,SLCO2B1,VNN1

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for LGMN

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00136	legumain	approved; nutraceutical	Calcitriol

Top

Cross referenced IDs for LGMN

* 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