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| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
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| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
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| Gene Summary for PGAM4 |
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| Phenotypic Information for PGAM4(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: PGAM4 |
| Familial Cancer Database: PGAM4 | |
| * 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_GLYCOLYSIS_GLUCONEOGENESIS | |
| Others | |
| OMIM | |
| Orphanet | |
| Disease | KEGG Disease: PGAM4 |
| MedGen: PGAM4 (Human Medical Genetics with Condition) | |
| ClinVar: PGAM4 | |
| Phenotype | MGI: PGAM4 (International Mouse Phenotyping Consortium) |
| PhenomicDB: PGAM4 | |
| Mutations for PGAM4 |
| * 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 PGAM4 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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: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
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| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=24) | (# total SNVs=8) |
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(# total SNVs=0) | (# total SNVs=0) |
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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 |
| chr23:77224704-77224704 | p.D144D | 3 |
| chr23:77224418-77224418 | p.C240R | 2 |
| chr23:77224638-77224638 | p.F166F | 2 |
| chr23:77224407-77224407 | p.I243M | 2 |
| chr23:77224872-77224872 | p.N88K | 1 |
| chr23:77224411-77224411 | p.A242D | 1 |
| chr23:77225074-77225074 | p.R21H | 1 |
| chr23:77224588-77224588 | p.I183S | 1 |
| chr23:77224878-77224878 | p.R86R | 1 |
| chr23:77225088-77225088 | p.W16C | 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 | 1 | 1 | 1 | 2 | 1 | 4 | 1 | 1 | 1 | 3 | 8 | |||||||||
| # mutation | 1 | 1 | 1 | 2 | 1 | 4 | 1 | 1 | 1 | 3 | 8 | |||||||||
| nonsynonymous SNV | 1 | 1 | 1 | 1 | 3 | 1 | 5 | |||||||||||||
| synonymous SNV | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 4 |
| 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 |
| chrX:77224704 | p.F166F | 2 |
| chrX:77224418 | p.D144D | 2 |
| chrX:77224638 | p.C240R | 2 |
| chrX:77224716 | p.L233L | 1 |
| chrX:77224439 | p.G34S | 1 |
| chrX:77224826 | p.N209N | 1 |
| chrX:77224509 | p.A33A | 1 |
| chrX:77224878 | p.E202Q | 1 |
| chrX:77224532 | p.R21H | 1 |
| chrX:77224951 | p.I193I | 1 |
| Other DBs for Point Mutations |
| Copy Number for PGAM4 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. |
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| 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 PGAM4 |
| 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. |
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| 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. |
: Open all plots for all cancer types
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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 |
: Open all plots for all cancer types
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| C10orf12,CHUK,CNOT1,DDX21,EIF2S1,EIF4G1,ERO1L, FAM45B,HSPA8,IARS,IDE,LDHA,LIMS1,LOC284441, MMS19,NOLC1,PGAM1,PGAM4,PGK1,PKM,RRAGC | ADAMTS2,ANXA2,ANXA2P1,ANXA2P2,CTNNA1,EXT2,FKBP9, GNA12,GPR153,ICMT,KDELR3,LASP1,PGAM1,PGAM4, PGD,PNMA1,PXDN,SAE1,SURF4,TMEM104,UNC13B |
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| ACTR3BP2,HSFX1,LCE2B,LOC653545,LOC728410,OR6N2,OR8B3, PGAM4,POTEE,PPIAL4B,PRAMEF17,PRAMEF3,RBMY1B,RPL13AP20, RPL13AP6,RPL21,RPS26P11,RPSAP9,SNORA38,SNORD104,SNORD16, SNORD35B,SNORD58C,SNORD62A,SNORD76,SNORD88B,SNORD88C,TPI1P3 | ASS1,CASP5,COX17,DYNLT1,ERP44,NEDD8,PGAM1, PGAM4,POMP,PPP1R7,PSMA3,PSMB3,PSMC1,PSMC4, SEC61B,SEC61G,SHFM1,SLC35B1,SOD1,SUGT1,TSPAN8 |
| 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 |
: Open all plots for all cancer types
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| Interacting 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 PGAM4 |
| There's no related Drug. |
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| Cross referenced IDs for PGAM4 |
| * 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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