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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PFDN5 |
Basic gene info. | Gene symbol | PFDN5 |
Gene name | prefoldin subunit 5 | |
Synonyms | MM-1|MM1|PFD5 | |
Cytomap | UCSC genome browser: 12q12 | |
Genomic location | chr12 :53689234-53693234 | |
Type of gene | protein-coding | |
RefGenes | NM_002624.3, NM_145897.2,NM_145896.2, | |
Ensembl id | ENSG00000123349 | |
Description | c-myc binding proteinmyc modulator-1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604899 | |
HGNC : HGNC | ||
Ensembl : ENSG00000123349 | ||
Vega : OTTHUMG00000169675 | ||
Protein | UniProt: Q99471 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PFDN5 | |
BioGPS: 5204 | ||
Gene Expression Atlas: ENSG00000123349 | ||
The Human Protein Atlas: ENSG00000123349 | ||
Pathway | NCI Pathway Interaction Database: PFDN5 | |
KEGG: PFDN5 | ||
REACTOME: PFDN5 | ||
ConsensusPathDB | ||
Pathway Commons: PFDN5 | ||
Metabolism | MetaCyc: PFDN5 | |
HUMANCyc: PFDN5 | ||
Regulation | Ensembl's Regulation: ENSG00000123349 | |
miRBase: chr12 :53,689,234-53,693,234 | ||
TargetScan: NM_002624 | ||
cisRED: ENSG00000123349 | ||
Context | iHOP: PFDN5 | |
cancer metabolism search in PubMed: PFDN5 | ||
UCL Cancer Institute: PFDN5 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of PFDN5 in cancer cell metabolism | 1. Zhang Pj, Wei R, Wen Xy, Ping L, Wang Cb, et al. (2012) Genes expression profiling of peripheral blood cells of patients with hepatocellular carcinoma. Cell biology international 36: 803-809. go to article |
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Phenotypic Information for PFDN5(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PFDN5 |
Familial Cancer Database: PFDN5 |
* 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_PROTEINS |
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OMIM | 604899; gene. |
Orphanet | |
Disease | KEGG Disease: PFDN5 |
MedGen: PFDN5 (Human Medical Genetics with Condition) | |
ClinVar: PFDN5 | |
Phenotype | MGI: PFDN5 (International Mouse Phenotyping Consortium) |
PhenomicDB: PFDN5 |
Mutations for PFDN5 |
* 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 PFDN5 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 |
AI351791 | CDK2AP2 | 15 | 480 | 11 | 67273968 | 67274432 | PFDN5 | 477 | 614 | 12 | 53689349 | 53689685 | |
CA307215 | PI4K2A | 18 | 537 | 10 | 99435289 | 99435808 | PFDN5 | 534 | 725 | 12 | 53691852 | 53693162 |
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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=11) | (# total SNVs=4) |
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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 |
chr12:53689386-53689386 | p.L12R | 3 |
chr12:53691830-53691830 | p.T95R | 1 |
chr12:53689707-53689707 | p.L53L | 1 |
chr12:53691896-53691896 | p.I117S | 1 |
chr12:53689715-53689715 | p.K55K | 1 |
chr12:53691907-53691907 | p.L121F | 1 |
chr12:53690048-53690048 | p.L66L | 1 |
chr12:53691936-53691936 | p.? | 1 |
chr12:53689355-53689355 | p.A2S | 1 |
chr12:53690060-53690060 | p.? | 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 |   |   | 2 |   |   |   |   | 1 |   |   | 1 | 2 | 2 |   | 1 |   | 3 |   | 1 |
# mutation | 1 |   |   | 2 |   |   |   |   | 1 |   |   | 1 | 2 | 2 |   | 1 |   | 3 |   | 1 |
nonsynonymous SNV |   |   |   | 1 |   |   |   |   | 1 |   |   | 1 | 1 | 2 |   | 1 |   | 2 |   |   |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   |   | 1 |   |   |   |   | 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 |
chr12:53691675 | p.I39V,PFDN5 | 1 |
chr12:53691676 | p.V41M,PFDN5 | 1 |
chr12:53691682 | p.T50R,PFDN5 | 1 |
chr12:53689355 | p.I72S,PFDN5 | 1 |
chr12:53691830 | p.L76F,PFDN5 | 1 |
chr12:53689386 | p.A2S,PFDN5 | 1 |
chr12:53691896 | p.L12R,PFDN5 | 1 |
chr12:53689395 | p.L15P,PFDN5 | 1 |
chr12:53691907 | p.L36L | 1 |
chr12:53689658 | p.L50L | 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 PFDN5 |
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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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ATP5G2,BLOC1S1,C12orf10,C12orf57,LAMTOR4,CCDC12,EDF1, MGMT,MRPL54,NDUFA2,PFDN5,RPL18,RPL29,RPL34, RPL36AL,RPL41,RPLP1,RPS14,RPS15,RPS9,WIBG | BUD31,CLTA,EIF3F,FAU,MRPS21,NME2,NSMCE1, PFDN5,RBMX2,RPL11,RPL24,RPL27A,RPL36,RPL36AL, RPL38,RPLP1,RPS11,RPS25,SARS,SNRPD2,SNRPF |
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C19orf53,EEF1B2,FAU,NDUFA13,OST4,PFDN5,RNF181, RPL24,RPL32,RPL35,RPL41,RPS10,RPS11,RPS14, RPS15A,RPS18,RPS3,RPS6,RPS7,RPS9,UBL5 | C18orf21,COMMD3,CWC15,DNAJC19,DPY30,FAU,FIS1, HAX1,HSCB,MRPL40,NFU1,OST4,PFDN5,RPL24, RPL35A,RPS13,RPS3A,RSL24D1,EMC4,TPT1,ZFAND1 |
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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 PFDN5 |
There's no related Drug. |
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Cross referenced IDs for PFDN5 |
* 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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