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 GPD1L
Basic gene info.Gene symbolGPD1L
Gene nameglycerol-3-phosphate dehydrogenase 1-like
SynonymsGPD1-L
CytomapUCSC genome browser: 3p22.3
Genomic locationchr3 :32148002-32210207
Type of geneprotein-coding
RefGenesNM_015141.3,
Ensembl idENSG00000152642
Descriptionglycerol-3-phosphate dehydrogenase 1-like protein
Modification date20141219
dbXrefs MIM : 611778
HGNC : HGNC
Ensembl : ENSG00000152642
HPRD : 10008
Vega : OTTHUMG00000155846
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPD1L
BioGPS: 23171
Gene Expression Atlas: ENSG00000152642
The Human Protein Atlas: ENSG00000152642
PathwayNCI Pathway Interaction Database: GPD1L
KEGG: GPD1L
REACTOME: GPD1L
ConsensusPathDB
Pathway Commons: GPD1L
MetabolismMetaCyc: GPD1L
HUMANCyc: GPD1L
RegulationEnsembl's Regulation: ENSG00000152642
miRBase: chr3 :32,148,002-32,210,207
TargetScan: NM_015141
cisRED: ENSG00000152642
ContextiHOP: GPD1L
cancer metabolism search in PubMed: GPD1L
UCL Cancer Institute: GPD1L
Assigned class in ccmGDBC

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Phenotypic Information for GPD1L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPD1L
Familial Cancer Database: GPD1L
* 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_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GPD1L
MedGen: GPD1L (Human Medical Genetics with Condition)
ClinVar: GPD1L
PhenotypeMGI: GPD1L (International Mouse Phenotyping Consortium)
PhenomicDB: GPD1L

Mutations for GPD1L
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasGPD1Lchr33216063132160651GPD1Lchr33216122132161241
pancreasGPD1Lchr33218654732186567GPD1Lchr33218681032186830
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPD1L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA778688ZEB211232145274917145277558GPD1L12355933214813432180220
BF849090GPD1L111933221001132210129UBE2G11134411742682094268537
BF849097GPD1L114533221001132210156UBE2G11394661742682094268537

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)          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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr3:32201101-32201101p.K298N2
chr3:32181857-32181857p.I168I1
chr3:32200531-32200531p.A261V1
chr3:32180207-32180207p.I118I1
chr3:32207311-32207311p.P322L1
chr3:32188164-32188164p.P186A1
chr3:32200539-32200539p.I264F1
chr3:32180216-32180216p.I121M1
chr3:32207339-32207339p.C331C1
chr3:32188173-32188173p.R189*1

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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
# sample11 61    1 61   36 4
# mutation11 71    1 71   36 4
nonsynonymous SNV1  5     1 71   33 3
synonymous SNV 1 21            3 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])

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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
chr3:32188176p.A115A1
chr3:32207310p.I264F1
chr3:32180198p.I118I1
chr3:32200400p.R281K1
chr3:32207311p.I121M1
chr3:32180207p.E288Q1
chr3:32200470p.I138I1
chr3:32207339p.R310H1
chr3:32180216p.R139H1
chr3:32200471p.F321Y1

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 GPD1L 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 GPD1L

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

C4orf32,SMIM14,CPEB3,DNAJC16,ELF1,FAM179B,FBXL5,
FOXA1,FYCO1,GPD1L,NUDT12,PDCD6IP,PGGT1B,RALGPS2,
RNF103,SPG11,STAM2,TMED7,TMEM87B,UEVLD,ZNF860
ABCB7,ATP5S,ADCK3,CHCHD10,FAM134B,GKAP1,GPD1L,
GPHN,L2HGDH,LRPPRC,MKNK2,OXA1L,PDHX,PDK2,
PPARA,SLC2A4,SUCLG2,TARSL2,TMLHE,UQCRC2,VDAC2

ANKRD28,SOWAHB,ATP10B,C10orf99,DLD,ENTPD5,EPB41L4B,
GPD1L,HOOK1,LARS2,LRRC31,MFN1,NGLY1,OXNAD1,
PDCD6IP,SATB2,SGK2,SLC16A9,SLC9A2,SNX4,SUCLG2
ACSS2,ATP6V1A,CAPN5,MCU,CDH17,RHOV___CHP1,CORO2A,
ABHD17C,GLTP,GPD1L,IQGAP2,LNX2,MARVELD2,NIPA2,
PAPSS2,PIP5K1B,PPP6C,PRR5L,RBM47,STYK1,TPRN
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 GPD1L


There's no related Drug.
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Cross referenced IDs for GPD1L
* 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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