|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PFDN4 |
Basic gene info. | Gene symbol | PFDN4 |
Gene name | prefoldin subunit 4 | |
Synonyms | C1|PFD4 | |
Cytomap | UCSC genome browser: 20q13.2 | |
Genomic location | chr20 :52824501-52836492 | |
Type of gene | protein-coding | |
RefGenes | NM_002623.3, | |
Ensembl id | ENSG00000101132 | |
Description | prefoldin 4protein C-1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604898 | |
HGNC : HGNC | ||
Ensembl : ENSG00000101132 | ||
HPRD : 05358 | ||
Vega : OTTHUMG00000032775 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PFDN4 | |
BioGPS: 5203 | ||
Gene Expression Atlas: ENSG00000101132 | ||
The Human Protein Atlas: ENSG00000101132 | ||
Pathway | NCI Pathway Interaction Database: PFDN4 | |
KEGG: PFDN4 | ||
REACTOME: PFDN4 | ||
ConsensusPathDB | ||
Pathway Commons: PFDN4 | ||
Metabolism | MetaCyc: PFDN4 | |
HUMANCyc: PFDN4 | ||
Regulation | Ensembl's Regulation: ENSG00000101132 | |
miRBase: chr20 :52,824,501-52,836,492 | ||
TargetScan: NM_002623 | ||
cisRED: ENSG00000101132 | ||
Context | iHOP: PFDN4 | |
cancer metabolism search in PubMed: PFDN4 | ||
UCL Cancer Institute: PFDN4 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for PFDN4(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: PFDN4 |
Familial Cancer Database: PFDN4 |
* 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/ |
![]() | |
REACTOME_METABOLISM_OF_PROTEINS |
![]() | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PFDN4 |
MedGen: PFDN4 (Human Medical Genetics with Condition) | |
ClinVar: PFDN4 | |
Phenotype | MGI: PFDN4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PFDN4 |
Mutations for PFDN4 |
* 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. |
![]() |
- Statistics for Tissue and Mutation type | Top |
![]() |
- 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'. |
![]() |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | PFDN4 | chr20 | 52830697 | 52830717 | PFDN4 | chr20 | 52825894 | 52825914 |
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) |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PFDN4 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 |
AV748690 | PFDN4 | 1 | 178 | 20 | 52833929 | 52834106 | PFDN4 | 173 | 336 | 20 | 52829676 | 52829849 |
![]() |
Top |
![]() |
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) |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=2) |
![]() | ![]() |
(# total SNVs=0) | (# total SNVs=0) |
Top |
![]() |
* 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 |
chr20:52830939-52830939 | p.K25T | 2 |
chr20:52830928-52830928 | p.Q21H | 1 |
chr20:52835638-52835638 | p.Q118H | 1 |
chr20:52830966-52830966 | p.T34I | 1 |
chr20:52830974-52830974 | p.K37E | 1 |
chr20:52830980-52830980 | p.E39* | 1 |
chr20:52830997-52830997 | p.K44N | 1 |
chr20:52831950-52831950 | p.E82K | 1 |
chr20:52831957-52831957 | p.Q84P | 1 |
chr20:52835581-52835581 | p.D99D | 1 |
Top |
![]() |
|
![]() |
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 |   |   |   | 3 | 1 |   |   |   | 2 |   |   |   |   |   |   |   | 2 | 1 |   | 2 |
# mutation |   |   |   | 3 | 1 |   |   |   | 2 |   |   |   |   |   |   |   | 2 | 1 |   | 2 |
nonsynonymous SNV |   |   |   | 3 | 1 |   |   |   | 1 |   |   |   |   |   |   |   | 1 | 1 |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   | 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]) |
Top |
![]() |
* 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 |
chr20:52830939 | p.K25T | 2 |
chr20:52830966 | p.K37E | 1 |
chr20:52830974 | p.E82K | 1 |
chr20:52831950 | p.Q84P | 1 |
chr20:52831957 | p.D99D | 1 |
chr20:52835581 | p.R104I | 1 |
chr20:52835595 | p.K116K | 1 |
chr20:52835632 | p.F123F | 1 |
chr20:52835653 | p.E18K | 1 |
chr20:52830917 | p.Q21H | 1 |
![]() |
![]() |
* 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] |
Top |
Gene Expression for PFDN4 |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* 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)) |
![]() |
Top |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* 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 |
![]() | |
ATP5E,ATP5EP2,AURKA,FAM210B,RTFDC1,CSTF1,DPM1, FAM96B,GNAS,NUTF2,PFDN4,PSMA7,RAB22A,RAE1, SLMO2,SNRPB2,STX16,NELFCD,TMEM189,UBE2C,UBE2V1 | C14orf166,C18orf21,C4orf27,C8orf59,CAMLG,CCDC58,CCDC59, COMMD6,COX7A2L,EIF3M,ESD,MFF,PFDN4,RAC1, RPS13,SNRPB2,SUMO1,TAF9,THOC7,TIMM9,TXNL1 |
![]() | |
ATP5E,C20orf24,RTFDC1,COMMD7,CTNNBL1,DPM1,DYNLRB1, EIF2S2,EIF6,ERGIC3,PDRG1,PFDN4,PIGU,PSMA7, RAE1,RALY,RPS21,SLMO2,NELFCD,TP53RK,UBE2V1 | ADH5,C4orf27,CAPZA2,COMMD2,DNAJC8,DYNLT3,FUNDC2, GTF2H5,MOB4,MORF4L1,NEK7,PFDN4,POLR2K,RHEB, RWDD1,SNAPIN,SPCS3,SUB1,SUMO2,UBA3,ZNF32 |
![]() |
* 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 |
Top |
![]() |
Top |
Pharmacological Information for PFDN4 |
There's no related Drug. |
Top |
Cross referenced IDs for PFDN4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |