|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LUM |
Basic gene info. | Gene symbol | LUM |
Gene name | lumican | |
Synonyms | LDC|SLRR2D | |
Cytomap | UCSC genome browser: 12q21.33 | |
Genomic location | chr12 :91497231-91505542 | |
Type of gene | protein-coding | |
RefGenes | NM_002345.3, | |
Ensembl id | ENSG00000139329 | |
Description | KSPG lumicankeratan sulfate proteoglycan lumicanlumican proteoglycan | |
Modification date | 20141207 | |
dbXrefs | MIM : 600616 | |
HGNC : HGNC | ||
HPRD : 02793 | ||
Protein | UniProt: P51884 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LUM | |
BioGPS: 4060 | ||
Gene Expression Atlas: ENSG00000139329 | ||
The Human Protein Atlas: ENSG00000139329 | ||
Pathway | NCI Pathway Interaction Database: LUM | |
KEGG: LUM | ||
REACTOME: LUM | ||
ConsensusPathDB | ||
Pathway Commons: LUM | ||
Metabolism | MetaCyc: LUM | |
HUMANCyc: LUM | ||
Regulation | Ensembl's Regulation: ENSG00000139329 | |
miRBase: chr12 :91,497,231-91,505,542 | ||
TargetScan: NM_002345 | ||
cisRED: ENSG00000139329 | ||
Context | iHOP: LUM | |
cancer metabolism search in PubMed: LUM | ||
UCL Cancer Institute: LUM | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
Top |
Phenotypic Information for LUM(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: LUM |
Familial Cancer Database: LUM |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
Oncogene 1 | Significant driver gene in GBM 6, |
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/ |
![]() | |
REACTOME_METABOLISM_OF_CARBOHYDRATES |
![]() | |
OMIM | 600616; gene. |
Orphanet | |
Disease | KEGG Disease: LUM |
MedGen: LUM (Human Medical Genetics with Condition) | |
ClinVar: LUM | |
Phenotype | MGI: 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. |
![]() |
There's no structural variation information in COSMIC data for this gene. |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LUM 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 |
AU100094 | SCCPDH | 8 | 95 | 1 | 246923505 | 246927610 | LUM | 94 | 300 | 12 | 91502648 | 91505251 | |
AI049509 | ZPBP | 9 | 33 | 7 | 50087251 | 50087275 | LUM | 25 | 186 | 12 | 91497325 | 91497493 | |
AW590716 | PABPC1L | 8 | 208 | 20 | 43570867 | 43571067 | LUM | 205 | 387 | 12 | 91502645 | 91505224 |
![]() |
Top |
![]() |
There's no copy number variation information in COSMIC data for this gene. |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=68) | (# total SNVs=4) |
![]() | ![]() |
(# total SNVs=1) | (# total SNVs=0) |
![]() |
Top |
![]() |
* 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 |
chr12:91502039-91502039 | p.E240K | 9 |
chr12:91497971-91497971 | p.R330C | 4 |
chr12:91498015-91498015 | p.R315H | 4 |
chr12:91502008-91502008 | p.S250C | 3 |
chr12:91502014-91502014 | p.G248E | 3 |
chr12:91498030-91498030 | p.R310H | 3 |
chr12:91502182-91502182 | p.S192N | 2 |
chr12:91502721-91502721 | p.L12L | 2 |
chr12:91502058-91502058 | p.Y233* | 2 |
chr12:91502421-91502421 | p.F112L | 2 |
Top |
![]() |
|
![]() |
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 |   | 2 |   | 15 | 7 |   | 1 |   | 2 |   |   | 13 | 3 |   |   |   | 14 | 7 |   | 11 |
# mutation |   | 2 |   | 11 | 6 |   | 1 |   | 2 |   |   | 13 | 2 |   |   |   | 14 | 6 |   | 14 |
nonsynonymous SNV |   | 2 |   | 10 | 6 |   |   |   | 1 |   |   | 12 | 2 |   |   |   | 9 | 4 |   | 13 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   | 1 |   |   | 1 |   |   |   |   | 5 | 2 |   | 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 |
![]() |
* 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 |
chr12:91502039 | p.E240K | 7 |
chr12:91497970 | p.F112L | 3 |
chr12:91502123 | p.R330H | 3 |
chr12:91497971 | p.R330C | 3 |
chr12:91502421 | p.L212L | 3 |
chr12:91498030 | p.R310H | 3 |
chr12:91502199 | p.S250Y | 2 |
chr12:91502246 | p.L186L | 2 |
chr12:91502008 | p.G248E | 2 |
chr12:91502014 | p.F112L | 2 |
![]() |
![]() |
* 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 |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* 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 |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* 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 |
![]() | |
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 |
![]() |
* 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 |
Top |
![]() |
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 |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |