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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GMPPA |
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Phenotypic Information for GMPPA(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GMPPA |
Familial Cancer Database: GMPPA |
* This gene is included in those cancer gene databases. |
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_FRUCTOSE_AND_MANNOSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GMPPA |
MedGen: GMPPA (Human Medical Genetics with Condition) | |
ClinVar: GMPPA | |
Phenotype | MGI: GMPPA (International Mouse Phenotyping Consortium) |
PhenomicDB: GMPPA |
Mutations for GMPPA |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GMPPA 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 |
Other DBs for Structural Variants |
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Copy 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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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=27) | (# total SNVs=7) |
(# total SNVs=1) | (# total SNVs=2) |
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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 |
chr2:220371039-220371039 | p.V353L | 2 |
chr2:220370456-220370456 | p.P291P | 2 |
chr2:220366625-220366625 | p.R99* | 2 |
chr2:220366626-220366626 | p.R99Q | 2 |
chr2:220371037-220371037 | p.R352L | 2 |
chr2:220368898-220368898 | p.R195W | 1 |
chr2:220364877-220364878 | p.P27fs*16 | 1 |
chr2:220370245-220370245 | p.A274G | 1 |
chr2:220366751-220366751 | p.G141S | 1 |
chr2:220371038-220371038 | p.R352R | 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 |   |   | 9 |   |   | 2 |   |   | 1 |   | 7 | 2 |   | 1 |   | 2 | 7 |   | 5 |
# mutation | 2 |   |   | 8 |   |   | 2 |   |   | 1 |   | 7 | 2 |   | 1 |   | 2 | 8 |   | 5 |
nonsynonymous SNV | 1 |   |   | 8 |   |   | 1 |   |   | 1 |   | 6 | 2 |   | 1 |   |   | 6 |   | 3 |
synonymous SNV | 1 |   |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 | 2 |   | 2 |
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 |
chr2:220368859 | p.R352P,GMPPA | 2 |
chr2:220371037 | p.G182S,GMPPA | 2 |
chr2:220371039 | p.V353L,GMPPA | 2 |
chr2:220371072 | p.D364Y,GMPPA | 2 |
chr2:220370189 | p.A395P,GMPPA | 1 |
chr2:220366242 | p.P61P,GMPPA | 1 |
chr2:220371440 | p.F198L,GMPPA | 1 |
chr2:220367155 | p.V397A,GMPPA | 1 |
chr2:220370238 | p.E85D,GMPPA | 1 |
chr2:220366585 | p.G212D,GMPPA | 1 |
Other DBs for Point Mutations |
Copy Number for GMPPA 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 GMPPA |
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 |
AP2S1,C19orf24,COPE,EDF1,FASTK,GMPPA,GUK1, MPG,MRPL55,NDUFA13,NUDT22,PHPT1,PPP1R7,RABAC1, RNF181,RNF25,RPS19BP1,SDF2L1,TRADD,ZFAND2B,ZNHIT1 | AGTRAP,ATP6V0B,C9orf142,CDK5,CHPF,COPE,GMPPA, GPR137,SLC52A2,GSS,LMAN2,LYPLA2,PIGQ,PPP4C, RABEP2,SDF2L1,SDSL,SIRT6,TEX264,TMEM208,TMEM54 |
AGR2,ANG,C19orf10,CIB1,COPG1,CRELD2,FKBP2, GMPPA,KCNK6,MANF,MRPL28,NUCB2,P4HB,PPIB, SLC50A1,RPN1,SDF2L1,SEC61A1,SLC39A7,TMED9,TMEM214 | ARF1,ARPC1A,ARPC1B,COASY,COPE,CYB561D2,GALE, GLYATL1,GMPPA,GMPPB,MED8,NAGLU,P4HB,PUSL1, SEC13,SLC35A2,SLC35B1,SLC39A7,TFG,TMED9,TMEM208 |
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 GMPPA |
There's no related Drug. |
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Cross referenced IDs for GMPPA |
* 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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