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 LGMN
Basic gene info.Gene symbolLGMN
Gene namelegumain
SynonymsAEP|LGMN1|PRSC1
CytomapUCSC genome browser: 14q32.1
Genomic locationchr14 :93170151-93215047
Type of geneprotein-coding
RefGenesNM_001008530.2,
NM_005606.6,
Ensembl idENSG00000100600
Descriptionasparaginyl endopeptidasecysteine protease 1protease, cysteine 1protease, cysteine, 1 (legumain)
Modification date20141207
dbXrefs MIM : 602620
HGNC : HGNC
Ensembl : ENSG00000100600
HPRD : 04017
Vega : OTTHUMG00000171199
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LGMN
BioGPS: 5641
Gene Expression Atlas: ENSG00000100600
The Human Protein Atlas: ENSG00000100600
PathwayNCI Pathway Interaction Database: LGMN
KEGG: LGMN
REACTOME: LGMN
ConsensusPathDB
Pathway Commons: LGMN
MetabolismMetaCyc: LGMN
HUMANCyc: LGMN
RegulationEnsembl's Regulation: ENSG00000100600
miRBase: chr14 :93,170,151-93,215,047
TargetScan: NM_001008530
cisRED: ENSG00000100600
ContextiHOP: LGMN
cancer metabolism search in PubMed: LGMN
UCL Cancer Institute: LGMN
Assigned class in ccmGDBC

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Phenotypic Information for LGMN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LGMN
MedGen: LGMN (Human Medical Genetics with Condition)
ClinVar: LGMN
PhenotypeMGI: LGMN (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LGMN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN269392RPL187510194911914149122421LGMN502618149317015493170270
AU138144LOC1005074121122?109636109757LGMN123661149318251693214972
AW450755COL6A3181002238232660238232742LGMN97368149317823693180796
AA157183LGMN185149321486893214953ENO186422189280608938673
BP392190LGMN1113149317615493178052VCAN11350158287674882877136
AW753026LGMN100261149318376693185212LGMN256482149318228993182515
BC008004VPS4A30998166935647669358908LGMN9992936149317015493214930

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      3          
GAIN (# sample)                 
LOSS (# sample)      3          
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=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.

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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
chr14:93185098-93185098p.S77F3
chr14:93170993-93170993p.P417P3
chr14:93180173-93180173p.R180R2
chr14:93178266-93178266p.S215S2
chr14:93199080-93199080p.V18I2
chr14:93182544-93182544p.L114R2
chr14:93179217-93179217p.?2
chr14:93170685-93170685p.H427H1
chr14:93172970-93172970p.R350H1
chr14:93183754-93183754p.Q97E1

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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
# sample   6  4 1  4    5616
# mutation   6  4 1  4    6716
nonsynonymous SNV   2  2 1  3    64 5
synonymous SNV   4  2    1     311
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
chr14:93178266p.S215S,LGMN2
chr14:93185138p.L339L,LGMN2
chr14:93176022p.E64K,LGMN2
chr14:93199105p.L9L,LGMN1
chr14:93170702p.K422Q,LGMN1
chr14:93176158p.A210A,LGMN1
chr14:93180777p.P417Q,LGMN1
chr14:93170994p.L402L,LGMN1
chr14:93176169p.L198M,LGMN1
chr14:93180791p.T397M,LGMN1

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 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]

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Gene Expression for LGMN

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

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
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 LGMN
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
DB00136legumainapproved; nutraceuticalCalcitriol


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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



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