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 LCT
Basic gene info.Gene symbolLCT
Gene namelactase
SynonymsLAC|LPH|LPH1
CytomapUCSC genome browser: 2q21
Genomic locationchr2 :136545414-136594750
Type of geneprotein-coding
RefGenesNM_002299.2,
Ensembl idENSG00000115850
Descriptionlactase-glycosylceramidaselactase-phlorizin hydrolaselactase-phlorizin hydrolase-1
Modification date20141207
dbXrefs MIM : 603202
HGNC : HGNC
Ensembl : ENSG00000115850
HPRD : 04437
Vega : OTTHUMG00000131738
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LCT
BioGPS: 3938
Gene Expression Atlas: ENSG00000115850
The Human Protein Atlas: ENSG00000115850
PathwayNCI Pathway Interaction Database: LCT
KEGG: LCT
REACTOME: LCT
ConsensusPathDB
Pathway Commons: LCT
MetabolismMetaCyc: LCT
HUMANCyc: LCT
RegulationEnsembl's Regulation: ENSG00000115850
miRBase: chr2 :136,545,414-136,594,750
TargetScan: NM_002299
cisRED: ENSG00000115850
ContextiHOP: LCT
cancer metabolism search in PubMed: LCT
UCL Cancer Institute: LCT
Assigned class in ccmGDBC

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Phenotypic Information for LCT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LCT
Familial Cancer Database: LCT
* 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
KEGG_GALACTOSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

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

Mutations for LCT
* 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 LCT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AY191611LCT135082136551907136570529MBTPS135093628168411591384116032
BF929873SSH214439172799509727995522LCT4394732136554299136554353

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              1  
GAIN (# sample)                 
LOSS (# sample)              1  
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=10

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=251)
Stat. for Synonymous SNVs
(# total SNVs=93)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=2)

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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
chr2:136567502-136567502p.F805F5
chr2:136566314-136566314p.A1201A5
chr2:136567238-136567238p.F893F4
chr2:136564712-136564712p.S1387P4
chr2:136555599-136555599p.R1659Q3
chr2:136566094-136566094p.G1275R3
chr2:136570154-136570154p.A694S3
chr2:136566069-136566069p.T1283R3
chr2:136567182-136567182p.S912F3
chr2:136564710-136564710p.S1387S3

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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=9

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample5113435 11 41 43227  4821223
# mutation5113485 11 41 50237  6926242
nonsynonymous SNV492343 8 21 40177  4016130
synonymous SNV121142 3 2  106   2910112
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
chr2:136564712p.S1387P4
chr2:136567238p.G1275R3
chr2:136564710p.S1387S3
chr2:136566094p.F893L3
chr2:136564885p.V716A2
chr2:136567187p.F984F2
chr2:136567447p.G910G2
chr2:136561527p.E1298Q2
chr2:136570187p.H658N2
chr2:136548388p.G1897G2

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 LCT 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 LCT

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

SMCO4,CEP128,ABRACL,CBR3,COQ3,ECE2,HELT,
HPDL,HRASLS,LCT,MCCC1,NDUFAF4,NOP58,NXPH4,
PSME4,SLC25A33,ST14,TIMM8A,TRPV6,UQCRH,UQCRHL
ACE2,VSTM5,CACNA1B,CES3,EPHA7,GGT3P,HAPLN3,
KCNN4,LCT,NALCN,OR51F2,PIWIL4,PSORS1C2,PTCHD2,
SLC10A2,SOX8,SPINK5,TBX10,TGFA,TRIM46,TUBA4B

AIM1,ANP32A,APOA4,APOB,CPO,DHX40P1,FMO9P,
GNRH2,KCNJ13,LCT,LRTM1,MCM6,MGAT4A,LINC01312,
OR1L4,OR2T35,OR7G2,RBMY3AP,REM2,SPANXN4,TNIP3
AGT,GGT1,GGT3P,GGTLC1,HEATR4,HTR4,KCP,
LAMB4,LCT,LEMD1,LPGAT1,OSBPL6,OSR2,PAEP,
RGS7BP,SEC16B,SERPINF2,SLC34A2,SSPO,UNC5CL,ZP2
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 LCT
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
DB00126lactaseapproved; nutraceuticalVitamin C
DB02376lactaseexperimentalD-Gluconhydroximo-1,5-Lactam
DB02471lactaseexperimentalNojirimycine Tetrazole
DB02944lactaseexperimentalAlpha-D-Mannose
DB03389lactaseexperimentalalpha-D-Xylopyranose
DB04282lactaseexperimental2-Deoxy-2fluoro-Glucose
DB04564lactaseexperimentalGluconolactone
DB04659lactaseexperimental(1S,2S,3R,4S,5S)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL (1E)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
DB04779lactaseexperimentalETHYL (1E)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
DB08558lactaseexperimental2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
DB04465lactaseexperimentalLactose


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Cross referenced IDs for LCT
* 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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