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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PGAM2 |
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Phenotypic Information for PGAM2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PGAM2 |
Familial Cancer Database: PGAM2 |
* 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/ |
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KEGG_GLYCOLYSIS_GLUCONEOGENESIS REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PGAM2 |
MedGen: PGAM2 (Human Medical Genetics with Condition) | |
ClinVar: PGAM2 | |
Phenotype | MGI: PGAM2 (International Mouse Phenotyping Consortium) |
PhenomicDB: PGAM2 |
Mutations for PGAM2 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | PGAM2 | chr7 | 44105114 | 44105134 | chr7 | 55782343 | 55782363 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PGAM2 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=14) | (# total SNVs=10) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 |
chr7:44104448-44104448 | p.I193T | 2 |
chr7:44104566-44104566 | p.E154Q | 2 |
chr7:44105092-44105092 | p.E13K | 2 |
chr7:44102513-44102513 | p.A204A | 2 |
chr7:44104839-44104839 | p.G97D | 1 |
chr7:44102368-44102368 | p.K253E | 1 |
chr7:44105053-44105053 | p.F26V | 1 |
chr7:44104495-44104495 | p.A177A | 1 |
chr7:44104852-44104852 | p.G93R | 1 |
chr7:44102378-44102378 | p.Q249Q | 1 |
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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 |   | 6 |   |   |   |   |   | 1 |   | 2 | 3 |   |   |   | 3 | 5 |   | 2 |
# mutation |   | 1 |   | 5 |   |   |   |   |   | 1 |   | 2 | 3 |   |   |   | 3 | 5 |   | 2 |
nonsynonymous SNV |   | 1 |   | 2 |   |   |   |   |   | 1 |   | 2 | 1 |   |   |   | 3 | 4 |   | 1 |
synonymous SNV |   |   |   | 3 |   |   |   |   |   |   |   |   | 2 |   |   |   |   | 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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* 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 |
chr7:44102513 | p.A204A | 2 |
chr7:44104599 | p.A143T | 2 |
chr7:44104771 | p.R86H | 1 |
chr7:44105125 | p.K253Q | 1 |
chr7:44102368 | p.D53H | 1 |
chr7:44104780 | p.Q249H | 1 |
chr7:44102378 | p.K49K | 1 |
chr7:44104787 | p.A247T | 1 |
chr7:44102386 | p.T35T | 1 |
chr7:44104827 | p.A242T | 1 |
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* 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 PGAM2 |
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* 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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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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BGLAP,MPLKIP,YAE1D1,CDH15,CPN2,DMP1,FLJ35390, FLJ46111,IBSP,IFITM5,MEPE,MT3,OR4C11,PGAM2, POLM,PRSS35,PTH1R,RASA4P,SLC36A2,SP7,URGCP | ABRA,ACTN2,AGBL1,ASB10,C10orf71,CACNA1S,ENO3, FBP2,FBXO40,LMOD3,MYF6,MYH4,MYL3,MYO18B, MYOT,PGAM2,PYGM,SLN,TECRL,TNNC2,UNC45B |
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ALX4,APOBEC2,BARHL1,CACNG3,CER1,CUX2,DKFZP434L187, FAM57B,GABRG2,GABRQ,GDAP1L1,KIRREL2,LHX3,MMD2, NTN3,PGAM2,PHF21B,SHISA7,SPANXD,SYT6,TMEM151B | BZRAP1,CACNG4,CCDC144B,CENPT,EGFL8,GIGYF1,HRNR, LOC100131691,LOC285033,LZTR1,MTA1,NPEPL1,NRBP2,PACS2, PEG3-AS1,PGAM2,PPIEL,PRR14,SGSM2,SLC2A11,TJAP1 |
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* 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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Pharmacological Information for PGAM2 |
There's no related Drug. |
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Cross referenced IDs for PGAM2 |
* 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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