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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMD12 |
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Phenotypic Information for PSMD12(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PSMD12 |
Familial Cancer Database: PSMD12 |
* 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/ |
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REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | 604450; gene. |
Orphanet | |
Disease | KEGG Disease: PSMD12 |
MedGen: PSMD12 (Human Medical Genetics with Condition) | |
ClinVar: PSMD12 | |
Phenotype | MGI: PSMD12 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMD12 |
Mutations for PSMD12 |
* 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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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMD12 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 |
BF064196 | ABAT | 354 | 392 | 16 | 8865884 | 8865922 | PSMD12 | 389 | 490 | 17 | 65351510 | 65351611 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=25) | (# total SNVs=11) |
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(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr17:65362552-65362552 | p.L28L | 4 |
chr17:65346383-65346383 | p.R123* | 2 |
chr17:65343510-65343510 | p.R201Q | 2 |
chr17:65340752-65340752 | p.W351C | 2 |
chr17:65344748-65344748 | p.A143V | 2 |
chr17:65353701-65353701 | p.? | 2 |
chr17:65341972-65341972 | p.A266V | 1 |
chr17:65346354-65346354 | p.T132T | 1 |
chr17:65337149-65337149 | p.S394L | 1 |
chr17:65343466-65343466 | p.E216K | 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 | 2 | 1 |   | 4 |   |   |   |   |   |   |   | 5 | 2 |   |   |   | 1 | 2 |   | 5 |
# mutation | 2 | 1 |   | 3 |   |   |   |   |   |   |   | 5 | 2 |   |   |   | 1 | 2 |   | 6 |
nonsynonymous SNV | 1 | 1 |   | 3 |   |   |   |   |   |   |   | 5 | 1 |   |   |   | 1 | 2 |   | 3 |
synonymous SNV | 1 |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | 3 |
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 |
chr17:65343510 | p.R181Q,PSMD12 | 2 |
chr17:65346353 | p.V267A,PSMD12 | 1 |
chr17:65340847 | p.S264S,PSMD12 | 1 |
chr17:65346408 | p.A246V,PSMD12 | 1 |
chr17:65340892 | p.S144S,PSMD12 | 1 |
chr17:65353488 | p.A143T,PSMD12 | 1 |
chr17:65341909 | p.L125L,PSMD12 | 1 |
chr17:65353523 | p.R124L,PSMD12 | 1 |
chr17:65341917 | p.M416I,PSMD12 | 1 |
chr17:65353674 | p.E113K,PSMD12 | 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 PSMD12 |
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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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AMZ2,BPTF,SMG8,CLTC,COIL,CYB561,GNA13, HELZ,KPNA2,LOC651250,MED13,METTL2A,MRPS23,NOL11, PPM1D,PRKAR1A,PSMD12,SKA2,SMURF2,TLK2,TRIM37 | BTBD1,CUL2,EIF2S1,FYTTD1,GFM1,KCMF1,KIAA1279, KPNA1,KPNA4,MAPK9,MRPS10,NAA50,PLAA,PPM1B, PSMC6,PSMD12,SLC16A1,SPPL2A,STAU2,TIMM17A,USP14 | ||||
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AMZ2,BOLA3,C17orf58,CCDC137,CCDC47,DCUN1D5,GPS1, KPNA2,METTL2A,MRPL12,NOL11,PIGW,PSMC5,PSMD11, PSMD12,PTRH2,RPS6KB1,TACO1,ALYREF,VMP1,TOMM40 | ACTR3,ARPC5L,BZW1,CHUK,DNAJB11,DNAJC3,ETF1, GNAI3,MAP2K4,NAMPT,PNP,PPP2CA,PPP2R2A,PSMB2, PSMC4,PSMD12,PSME3,RAB1A,SEC61G,SSR1,UBQLN1 |
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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 PSMD12 |
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DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA33903; -. |
Organism-specific databases | CTD | 5718; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00171 | proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 | approved; nutraceutical | Adenosine triphosphate | ![]() | ![]() |
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Cross referenced IDs for PSMD12 |
* 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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