Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 GLIPR1
Basic gene info.Gene symbolGLIPR1
Gene nameGLI pathogenesis-related 1
SynonymsCRISP7|GLIPR|RTVP1
CytomapUCSC genome browser: 12q21.2
Genomic locationchr12 :75874512-75895716
Type of geneprotein-coding
RefGenesNM_006851.2,
Ensembl idENSG00000139278
DescriptionGLI pathogenesis-related 1 (glioma)gliPR 1glioma pathogenesis-related protein 1protein RTVP-1related to testis-specific, vespid, and pathogenesis proteins 1testes-specific vespid and pathogenesis protein 1
Modification date20141207
dbXrefs MIM : 602692
HGNC : HGNC
HPRD : 04071
ProteinUniProt: P48060
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GLIPR1
BioGPS: 11010
Gene Expression Atlas: ENSG00000139278
The Human Protein Atlas: ENSG00000139278
PathwayNCI Pathway Interaction Database: GLIPR1
KEGG: GLIPR1
REACTOME: GLIPR1
ConsensusPathDB
Pathway Commons: GLIPR1
MetabolismMetaCyc: GLIPR1
HUMANCyc: GLIPR1
RegulationEnsembl's Regulation: ENSG00000139278
miRBase: chr12 :75,874,512-75,895,716
TargetScan: NM_006851
cisRED: ENSG00000139278
ContextiHOP: GLIPR1
cancer metabolism search in PubMed: GLIPR1
UCL Cancer Institute: GLIPR1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GLIPR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GLIPR1
Familial Cancer Database: GLIPR1
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602692; gene.
Orphanet
DiseaseKEGG Disease: GLIPR1
MedGen: GLIPR1 (Human Medical Genetics with Condition)
ClinVar: GLIPR1
PhenotypeMGI: GLIPR1 (International Mouse Phenotyping Consortium)
PhenomicDB: GLIPR1

Mutations for GLIPR1
* 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 GLIPR1 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11            1  
GAIN (# sample)11            1  
LOSS (# sample)                 
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr12:75874745-75874745p.E29K3
chr12:75875683-75875683p.R82R3
chr12:75875797-75875797p.E120K2
chr12:75892747-75892747p.L264I2
chr12:75874698-75874698p.S13Y2
chr12:75884218-75884218p.C151C2
chr12:75875776-75875776p.A113T1
chr12:75874744-75874744p.I28I1
chr12:75884247-75884247p.G161V1
chr12:75875650-75875650p.W71R1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 51 2 2  6 1  81 7
# mutation12 51 2 2  6 1  61 7
nonsynonymous SNV12 41 2 1  5 1  51 4
synonymous SNV   1    1  1    1  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
chr12:75874745p.E29K3
chr12:75875797p.E120K2
chr12:75884201p.R82W1
chr12:75875711p.G176E1
chr12:75884218p.R82R1
chr12:75874778p.G189R1
chr12:75875727p.P91Q1
chr12:75884247p.R211Q1
chr12:75874782p.L96L1
chr12:75875733p.P223A1

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 GLIPR1 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 GLIPR1

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

ACSL4,ADAM19,ANTXR2,ARHGAP31,ARSB,EOGT,CALD1,
CARD6,DPYSL3,DSE,ETS1,FAS,GLIPR1,KCTD12,
LIX1L,MSN,PLS3,QKI,STARD4,VIM,ZEB2
ACTR3,ARPC5,SLC18B1,CLEC7A,EVI2A,FAS,GLIPR1,
IFI16,LYN,MFSD1,MYD88,PPP4R1,PTPLAD2,PTPRE,
SAMSN1,SEC24D,SERPINB8,SGMS2,SYK,TMEM200A,TPM4

BBOX1,C17orf78,CALCB,CLDN22,COL6A5,CYP17A1,CYP7A1,
GLIPR1,INSC,MEP1B,NLRP6,NR1H4,NRCAM,OSTalpha,
PDK1,SERPINE3,SLC7A9,SPAM1,TBX3,TM6SF2,TMEM229A
ANXA1,BBS4,C11orf73,FAM216A,C1orf54,C20orf27,CAMK1,
CYB5R1,FAM92A1,GLIPR1,GNG11,IGFBP7,IKBIP,ITGB1BP1,
MPV17,PPT1,SGTB,SNAPIN,TMSB15B,TRMT112,TTC8
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 GLIPR1


There's no related Drug.
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Cross referenced IDs for GLIPR1
* 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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