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 LEP
Basic gene info.Gene symbolLEP
Gene nameleptin
SynonymsLEPD|OB|OBS
CytomapUCSC genome browser: 7q31.3
Genomic locationchr7 :127881330-127897682
Type of geneprotein-coding
RefGenesNM_000230.2,
Ensembl idENSG00000174697
Descriptionleptin (murine obesity homolog)leptin (obesity homolog, mouse)obese proteinobese, mouse, homolog ofobesity factor
Modification date20141222
dbXrefs MIM : 164160
HGNC : HGNC
Ensembl : ENSG00000174697
HPRD : 01249
Vega : OTTHUMG00000157564
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LEP
BioGPS: 3952
Gene Expression Atlas: ENSG00000174697
The Human Protein Atlas: ENSG00000174697
PathwayNCI Pathway Interaction Database: LEP
KEGG: LEP
REACTOME: LEP
ConsensusPathDB
Pathway Commons: LEP
MetabolismMetaCyc: LEP
HUMANCyc: LEP
RegulationEnsembl's Regulation: ENSG00000174697
miRBase: chr7 :127,881,330-127,897,682
TargetScan: NM_000230
cisRED: ENSG00000174697
ContextiHOP: LEP
cancer metabolism search in PubMed: LEP
UCL Cancer Institute: LEP
Assigned class in ccmGDBC

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

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

Mutations for LEP
* 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 LEP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=13)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr7:127894591-127894591p.N93N2
chr7:127894720-127894720p.E136D2
chr7:127894744-127894744p.V144V1
chr7:127892092-127892092p.C7C1
chr7:127894638-127894638p.H109L1
chr7:127894749-127894749p.A146G1
chr7:127892093-127892093p.G8R1
chr7:127894639-127894639p.H109Q1
chr7:127894784-127894784p.L158L1
chr7:127892098-127892098p.F9L1

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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  13  1 1  8    41 5
# mutation  13  1 1  9    41 5
nonsynonymous SNV  11  1 1  6    2  2
synonymous SNV   2       3    21 3
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
chr7:127892098p.F9L2
chr7:127894591p.N93N2
chr7:127894784p.G8R1
chr7:127892093p.G124S1
chr7:127894615p.E126E1
chr7:127894809p.L12I1
chr7:127894638p.T127A1
chr7:127892105p.P23P1
chr7:127894641p.V134V1
chr7:127892140p.S53S1

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 LEP 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 LEP

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

AOC3,AQP7,AQP7P1,C14orf180,CD300LG,CIDEC,FABP4,
GLYAT,GPAM,GPD1,HEPACAM,HEPN1,ITIH5,KCNIP2,
KLB,LEP,LIPE,PLIN1,PLIN4,RDH5,SLC22A12
ANGPT1,ASPH,BHMT2,NPR3,CES1,CHRDL1,DHDDS,
GCOM1,GLYAT,GNG2,GNS,GPLD1,ITIH5,ITSN1,
LEP,NMT2,PYGL,RASA3,RHOQ,STS,TNS3

ACSM5,ADH1B,ADIPOQ,AQP7,CD300LG,CD36,EPB42,
FABP4,GLYAT,HEPACAM,KCNIP2,LEP,LIPE,MRAP,
PCOLCE2,PLIN1,PLIN4,PTCHD3,SCN4A,SGCG,TUSC5
AACSP1,ADIPOQ,LINC00301,CLPSL2,C7orf34,C9orf47,CIDEA,
DEFB132,FABP4,SPATA31D1,GLYAT,HSFY2,KCNIP2,LEP,
LIPE,LOC388387,MRAP,OR52D1,PLIN1,S100G,TAAR8,
TUSC5,USP1
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 LEP
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
DB00734leptinapproved; investigationalRisperidone
DB01041leptinapproved; withdrawn; investigationalThalidomide
DB00334leptinapproved; investigationalOlanzapine
DB00898leptinapprovedEthanol


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Cross referenced IDs for LEP
* 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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