Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 LUM
Basic gene info.Gene symbolLUM
Gene namelumican
SynonymsLDC|SLRR2D
CytomapUCSC genome browser: 12q21.33
Genomic locationchr12 :91497231-91505542
Type of geneprotein-coding
RefGenesNM_002345.3,
Ensembl idENSG00000139329
DescriptionKSPG lumicankeratan sulfate proteoglycan lumicanlumican proteoglycan
Modification date20141207
dbXrefs MIM : 600616
HGNC : HGNC
HPRD : 02793
ProteinUniProt: P51884
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LUM
BioGPS: 4060
Gene Expression Atlas: ENSG00000139329
The Human Protein Atlas: ENSG00000139329
PathwayNCI Pathway Interaction Database: LUM
KEGG: LUM
REACTOME: LUM
ConsensusPathDB
Pathway Commons: LUM
MetabolismMetaCyc: LUM
HUMANCyc: LUM
RegulationEnsembl's Regulation: ENSG00000139329
miRBase: chr12 :91,497,231-91,505,542
TargetScan: NM_002345
cisRED: ENSG00000139329
ContextiHOP: LUM
cancer metabolism search in PubMed: LUM
UCL Cancer Institute: LUM
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for LUM(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LUM
Familial Cancer Database: LUM
* 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 GBM 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.sciencedirect.com/science/article/pii/S0092867413012087,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 600616; gene.
Orphanet
DiseaseKEGG Disease: LUM
MedGen: LUM (Human Medical Genetics with Condition)
ClinVar: LUM
PhenotypeMGI: LUM (International Mouse Phenotyping Consortium)
PhenomicDB: LUM

Mutations for LUM
* 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 LUM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AU100094SCCPDH8951246923505246927610LUM94300129150264891505251
AI049509ZPBP93375008725150087275LUM25186129149732591497493
AW590716PABPC1L8208204357086743571067LUM205387129150264591505224

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=8

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=68)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr12:91502039-91502039p.E240K9
chr12:91497971-91497971p.R330C4
chr12:91498015-91498015p.R315H4
chr12:91502008-91502008p.S250C3
chr12:91502014-91502014p.G248E3
chr12:91498030-91498030p.R310H3
chr12:91497970-91497970p.R330H2
chr12:91502423-91502423p.F112L2
chr12:91502123-91502123p.L212L2
chr12:91497982-91497982p.Y326F2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 157 1 2  133   147 11
# mutation 2 116 1 2  132   146 14
nonsynonymous SNV 2 106   1  122   94 13
synonymous SNV   1  1 1  1    52 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
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
chr12:91502039p.E240K7
chr12:91497970p.R330H3
chr12:91502123p.R330C3
chr12:91497971p.R310H3
chr12:91502421p.L212L3
chr12:91498030p.F112L3
chr12:91502246p.F112L2
chr12:91502008p.L171M2
chr12:91502014p.R315H2
chr12:91502721p.L12L2

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 LUM 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 LUM

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))
Top
check002.gifCNV 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
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

ANTXR1,CDH11,COL10A1,COL12A1,COL5A2,DACT1,DCN,
ECM2,FAM26E,FAP,FBN1,GLT8D2,ITGBL1,LRRC15,
LUM,MFAP5,MXRA5,NOX4,OLFML1,RECK,THBS2
ASPN,BASP1,CCDC109B,CTHRC1,CTSK,DCN,FAP,
GPX8,LRRC17,LUM,LY96,MFAP2,MMP2,NT5E,
OGN,PDGFRL,PTPLAD2,SFRP2,SFRP4,TMEM119,TPST1

ANTXR1,C1S,CERCAM,CTHRC1,CTSK,DCN,EFEMP2,
FSTL1,GLT8D2,LUM,MXRA8,OLFML1,PCOLCE,PDGFRB,
PRRX1,RAB31,SDC2,SERPINF1,SPARC,SULF1,THY1
CCDC80,CXCL12,DCN,FKBP10,GALNT11,GALNT16,GLT8D2,
GPX8,HTRA1,KCNE4,LHFP,LRRN4CL,LUM,OGN,
OLFML3,RBMS1,SNCG,SRPX,THBS2,THY1,SLC35G2
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for LUM


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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas