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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPD2 |
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Phenotypic Information for GPD2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPD2 |
Familial Cancer Database: GPD2 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GPD2 |
MedGen: GPD2 (Human Medical Genetics with Condition) | |
ClinVar: GPD2 | |
Phenotype | MGI: GPD2 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPD2 |
Mutations for GPD2 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | GPD2 | chr2 | 157332093 | 157332113 | GPD2 | chr2 | 157332246 | 157332266 |
ovary | GPD2 | chr2 | 157364321 | 157364341 | chr7 | 44538570 | 44538590 | |
ovary | GPD2 | chr2 | 157379452 | 157379472 | chr2 | 157462007 | 157462027 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPD2 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 |
BF310332 | ENY2 | 18 | 501 | 8 | 110348356 | 110355893 | GPD2 | 497 | 519 | 2 | 157375189 | 157375211 | |
BE815959 | GPD2 | 1 | 239 | 2 | 157336335 | 157336573 | RASAL2 | 231 | 557 | 1 | 178412304 | 178412630 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=48) | (# total SNVs=14) |
(# total SNVs=1) | (# total SNVs=1) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr2:157439371-157439371 | p.E709Q | 2 |
chr2:157407127-157407127 | p.D280D | 2 |
chr2:157439395-157439395 | p.P717S | 2 |
chr2:157413986-157413986 | p.G353C | 2 |
chr2:157352693-157352693 | p.T80T | 2 |
chr2:157407174-157407174 | p.S296Y | 2 |
chr2:157427707-157427707 | p.R557H | 2 |
chr2:157406249-157406249 | p.R264H | 2 |
chr2:157439370-157439370 | p.A708A | 2 |
chr2:157367411-157367411 | p.I126I | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 2 |   | 10 | 2 |   | 2 |   | 1 | 1 |   | 8 | 3 | 3 | 1 |   | 4 | 9 | 2 | 4 |
# mutation | 2 | 2 |   | 10 | 2 |   | 2 |   | 1 | 1 |   | 8 | 3 | 3 | 1 |   | 4 | 9 | 2 | 4 |
nonsynonymous SNV | 1 | 1 |   | 8 | 1 |   | 2 |   |   |   |   | 7 | 2 | 2 | 1 |   | 2 | 5 | 1 | 3 |
synonymous SNV | 1 | 1 |   | 2 | 1 |   |   |   | 1 | 1 |   | 1 | 1 | 1 |   |   | 2 | 4 | 1 | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr2:157407174 | p.S296Y,GPD2 | 2 |
chr2:157439371 | p.E709K,GPD2 | 2 |
chr2:157406241 | p.T294M,GPD2 | 1 |
chr2:157435477 | p.T447T,GPD2 | 1 |
chr2:157407246 | p.L687L,GPD2 | 1 |
chr2:157332647 | p.N449H,GPD2 | 1 |
chr2:157426037 | p.A708V,GPD2 | 1 |
chr2:157407115 | p.T10T,GPD2 | 1 |
chr2:157435653 | p.R298C,GPD2 | 1 |
chr2:157414015 | p.G488A,GPD2 | 1 |
Other DBs for Point Mutations |
Copy Number for GPD2 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 GPD2 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
AFTPH,CD46,CHM,CSNK1G1,DNAJC16,GPD2,IPP, CERS6,PJA2,RAB3GAP1,RFX7,SCRN3,SPATA6,SPG11, SRBD1,STAM2,TMED7,TMEM87B,UBR3,UBXN4,XIAP | AP1G1,DNAJC16,ERBB2IP,FNBP1L,GPD2,KRR1,METTL15, MPP5,NAA25,NAA35,NUPL1,PIGN,SLC30A9,TFAM, UBXN4,USP37,VPS36,WAPAL,ZDHHC21,ZNF24,ZNF770 |
ASAP2,BCL10,CNNM4,DIAPH1,GALNT5,GPD2,JOSD1, KLF3,LGR4,LIPH,MALL,PLS1,PRRG4,PTPRH, RBM47,SHROOM3,SLC25A24,SPOPL,SSFA2,STYK1,TSPAN1 | ACTR2,B4GALT1,BAZ1A,CCDC186,CHD1,DSC2,F11R, GPD2,KIF16B,MIER3,NIPA2,NT5C2,PDCD6IP,PPP2R1B, RAB14,RBM47,RNF6,TMOD3,XIAP,YWHAB,ZNF326 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GPD2 |
There's no related Drug. |
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Cross referenced IDs for GPD2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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