Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PFDN1
Basic gene info.Gene symbolPFDN1
Gene nameprefoldin subunit 1
SynonymsPDF|PFD1
CytomapUCSC genome browser: 5q31
Genomic locationchr5 :139624634-139682689
Type of geneprotein-coding
RefGenesNM_002622.4,
Ensembl idENSG00000113068
Descriptionprefoldin 1
Modification date20141207
dbXrefs MIM : 604897
HGNC : HGNC
Ensembl : ENSG00000113068
HPRD : 05357
Vega : OTTHUMG00000129249
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PFDN1
BioGPS: 5201
Gene Expression Atlas: ENSG00000113068
The Human Protein Atlas: ENSG00000113068
PathwayNCI Pathway Interaction Database: PFDN1
KEGG: PFDN1
REACTOME: PFDN1
ConsensusPathDB
Pathway Commons: PFDN1
MetabolismMetaCyc: PFDN1
HUMANCyc: PFDN1
RegulationEnsembl's Regulation: ENSG00000113068
miRBase: chr5 :139,624,634-139,682,689
TargetScan: NM_002622
cisRED: ENSG00000113068
ContextiHOP: PFDN1
cancer metabolism search in PubMed: PFDN1
UCL Cancer Institute: PFDN1
Assigned class in ccmGDBC

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Phenotypic Information for PFDN1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PFDN1
Familial Cancer Database: PFDN1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PFDN1
MedGen: PFDN1 (Human Medical Genetics with Condition)
ClinVar: PFDN1
PhenotypeMGI: PFDN1 (International Mouse Phenotyping Consortium)
PhenomicDB: PFDN1

Mutations for PFDN1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PFDN1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr5:139625615-139625615p.V105I1
chr5:139682629-139682629p.K10N1
chr5:139625621-139625621p.R103*1
chr5:139682658-139682658p.M1V1
chr5:139661036-139661036p.E95*1
chr5:139661085-139661085p.S78S1
chr5:139680061-139680061p.T47K1
chr5:139680081-139680081p.T40T1
chr5:139680082-139680082p.T40M1
chr5:139680100-139680100p.I34S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   4       2       2
# mutation   4       2       2
nonsynonymous SNV   2       1       2
synonymous SNV   2       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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr5:139680061p.T47K1
chr5:139680081p.T40T1
chr5:139680082p.T40M1
chr5:139680105p.I32I1
chr5:139680111p.A30A1
chr5:139680113p.A30T1
chr5:139682658p.M1V1
chr5:139625615p.V105I1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for PFDN1 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.
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 PFDN1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ATP5G2,CYSTM1,COX7C,HARS,HIGD2A,IK,MED7,
MRPL22,MRPS36,NDUFA2,NDUFB4,PFDN1,PPP2CA,RPL26L1,
SLC35A4,SRA1,SRP19,TBCA,TTC1,UBE2D2,UQCRQ
ATP5E,ATP5H,ATP5J,ATP6V1E1,EMC7,C1orf123,ATRAID,
CYSTM1,GTF3A,HINT2,IAH1,MGST3,MSRB2,CMC4,
PFDN1,PSMB1,PSMC1,SNAPIN,STX8,TTC1,UBE2L3

ATP6V0E1,CCNH,HARS,HINT1,MED7,MRPL22,MRPS36,
NDFIP1,NDUFA2,NDUFB4,PFDN1,PPP2CA,RPL26L1,SKP1,
SRA1,TAF9,TBCA,TTC1,UBE2B,UBE2D2,UQCRQ
C11orf58,BRK1,COPS2,DNAJC8,FBXL5,FUNDC2,KATNA1,
MANBAL,MOCS2,MORF4L1,PCGF6,PFDN1,RWDD1,RWDD2B,
SNAPIN,SNX3,TCEAL8,TPD52L2,UROD,ZCCHC17,ZNF32
check002.gifCo-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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check002.gifInteracting 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 PFDN1


There's no related Drug.
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Cross referenced IDs for PFDN1
* 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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