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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: PDF (NCBI Gene ID:64146)

Gene Summary

Gene Summary

Gene Information	Gene Name: PDF
	Gene ID: 64146
	Gene Symbol	PDF
	Gene ID	64146
	Gene Name	peptide deformylase, mitochondrial
	Synonyms	-
	Cytomap	16q22.1
	Type of Gene	protein-coding
	Description	peptide deformylase, mitochondrialpeptide deformylase-like proteinpolypeptide deformylase
	Modification date	20200313
	UniProtAcc	Q9HBH1

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	PDF	GO:0018206	peptidyl-methionine modification	15489958
Hgene	PDF	GO:0031365	N-terminal protein amino acid modification	15489958

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
PDF	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'PDF[title] AND translation [title] AND human.'

Gene	Title	PMID
PDF	.	.

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST

Exon skip start (DNA)

Exon Skip end (DNA)

ORF

Exon skipping position in the amino acid sequence.

ENST

Exon skip start (DNA)

Exon Skip end (DNA)

Len(transcript seq)

Exon skip start (mRNA)

Exon Skip end (mRNA)

Len(amino acid seq)

Exon skip start (AA)

Exon Skip end (AA)

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc

Exon skip start (AA)

Exon Skip end (AA)

Function feature start (AA)

Function feature end (AA)

Functional feature type

Functional feature desc.

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
PRAD	PDF	-1.83573074557218	0.00211503858224308
CHOL	PDF	-2.35440894163977	0.00390625
KIRC	PDF	-2.08272493094078	0.00724874285490747
BRCA	PDF	-1.85666700432586	2.87720383141203e-13
LUSC	PDF	-2.24754662802234	5.69044796414887e-09
LUAD	PDF	-2.8456821603014	8.2686862267444e-10
KIRP	PDF	1.28164472282644	9.99853946268559e-05

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type	Gene	miRNA	TargetScan binding score (Context++ score percentile)	Coefficient	Pvalue
DLBC	PDF	hsa-miR-339-5p	76	0.315564292321924	0.0311713710863107

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type	Gene	methyl group b	methyl group a	DEG pval	avg methyl in b	avg methyl in a	avg exp in b	avg exp in a
LUSC	PDF	3	2	0.0328481334538724	0.651783311993171	0.561552254831783	0.142003628779852	0.0187053255748753

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
DLBC	PDF	-0.027399791	0.010762257
UCS	PDF	-0.03986277	0.024215263
UVM	PDF	-0.110425587	0.026233559
LUSC	PDF	0.07341406	0.042090177

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with PDF (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
CHOL	Cell metabolism gene	PDF	SLC25A10	0.804453822	2.79E-11
CHOL	IUPHAR	PDF	SLC25A10	0.804453822	2.79E-11
DLBC	Cell metabolism gene	PDF	SNRPD3	0.802975212	6.61E-12
DLBC	Cell metabolism gene	PDF	ADSL	0.813556938	2.10E-12
DLBC	Cell metabolism gene	PDF	TIMM13	0.814464803	1.90E-12
DLBC	Cell metabolism gene	PDF	EXOSC4	0.823156507	6.95E-13
DLBC	Cell metabolism gene	PDF	TIMM50	0.837661788	1.15E-13
DLBC	Cell metabolism gene	PDF	TOMM22	0.856694683	8.08E-15
DLBC	Epifactor	PDF	EXOSC4	0.823156507	6.95E-13
DLBC	IUPHAR	PDF	MFSD2B	0.801831808	7.45E-12
DLBC	TSG	PDF	GADD45GIP1	0.81463659	1.86E-12
DLBC	TSG	PDF	PHB	0.81792698	1.28E-12
THYM	Cell metabolism gene	PDF	MED27	0.805063965	5.45E-29
THYM	Cell metabolism gene	PDF	POLR2I	0.812085345	7.56E-30
THYM	Cell metabolism gene	PDF	HSD17B10	0.833973256	8.97E-33
THYM	Cell metabolism gene	PDF	APRT	0.839150735	1.58E-33
UCS	Cell metabolism gene	PDF	MED27	0.805063965	5.45E-29
UCS	Cell metabolism gene	PDF	POLR2I	0.812085345	7.56E-30
UCS	Cell metabolism gene	PDF	HSD17B10	0.833973256	8.97E-33
UCS	Cell metabolism gene	PDF	APRT	0.839150735	1.58E-33

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
KIRC	PDF	MRPL20	1.48585631024503	0.000111704804180407
KIRC	PDF	MRPL11	-1.04966837625557	0.000354478033746394
LUAD	PDF	MRPL20	-3.00071204707904	0.000452706327224566
BRCA	PDF	MRPL20	-1.74379528461375	0.000756034430433012
KICH	PDF	TSFM	1.15779807454151	0.00129634141921997
KICH	PDF	MRRF	1.86992130954506	0.0014527440071106
KIRP	PDF	METAP2	1.2125553034505	0.00166679499670863
ESCA	PDF	MRPL17	-1.18756178214998	0.009765625
KIRP	PDF	METAP1	1.245174280985	0.0111397774890065
LIHC	PDF	MRPL17	-1.06225729770915	0.0124123499319886
LIHC	PDF	MRPL20	-1.08735154161025	0.0158079482509981
LIHC	PDF	MRRF	-1.19805818879659	0.0305924082275009
KICH	PDF	MTFMT	2.05895643036764	1.13248825073242e-06
PRAD	PDF	MRPL11	1.12581653394628	1.15996224044503e-05
LUSC	PDF	TSFM	-3.83005339359833	1.4433166414012e-09
LUSC	PDF	MRPL21	-4.98277643789037	1.45947399043856e-08
STAD	PDF	MRPL17	-3.90880705449186	1.49570405483246e-06
PRAD	PDF	MRRF	-1.56810957454655	2.74398347191128e-05
BRCA	PDF	TSFM	-2.93602416019673	2.90907687062967e-14
LUAD	PDF	MRPL21	-1.86897497221853	6.16191557420719e-07
LUSC	PDF	MRPL17	-6.83409683292749	6.93230040561614e-07
BRCA	PDF	MRPL21	-1.5345447607194	7.40794680786486e-08
LUAD	PDF	TSFM	-4.00047669194892	9.20176185683847e-09

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with PDF

ZPBP2, IDS, ERBB3, TMEM25, PTCH1, OLFM4, CENPA, SRPR, TSNAX, SLC33A1, TACC3, SGTB, HAUS2, RNASEH2B, ACTR5, PARD6B, BAG6, Smc3, Max, Nek2, Sart1, Cdc6, Smc1a, Cdc23, Mad2l1, Shoc2, Tsc1, Trip11, Oxnad1, Rab3gap1, Tnpo1, KIF1B, CRP, MRPS34, P4HA3, A2M, CETN1, PROC, DEFA5, MMP26, NPPA, NRROS, ENPP7, ADAM21, ADAM33, TFR2, BPNT1, MYO5B, RAC1, ESR2, HSCB, ARHGEF11, DDX39A, RNF7, CCL3, HFE, EFNA2, CALM1, ECEL1, MCOLN2, GPSM3, PDGFRA, S100A2, SCGB2A2, ELFN2, SPX, UQCRFS1, IFNG, MOB2, TFDP2, ZDHHC23, STAT2, PDE7A, BBOX1, BTF3, SSMEM1, RAB24, GTF2E2, GKN1, IL23R, PRSS48, CCNF,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
PDF	chr16	69362541	C	A	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362603	G	A	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362617	G	A	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362707	T	C	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362777	T	A	single_nucleotide_variant	Benign	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362779	C	A	single_nucleotide_variant	Benign	Congenital_disorder_of_glycosylation_type_2H	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69362912	C	CA	Duplication	Uncertain_significance	Congenital_disorder_of_glycosylation	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PDF	chr16	69363036	C	T	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001587\|nonsense,SO:0001624\|3_prime_UTR_variant	SO:0001587\|nonsense,SO:0001624\|3_prime_UTR_variant
PDF	chr16	69363089	AG	A	Deletion	Likely_benign	not_specified	SO:0001627\|intron_variant	SO:0001627\|intron_variant
PDF	chr16	69364173	G	A	single_nucleotide_variant	Uncertain_significance	Congenital_disorder_of_glycosylation_type_2H	SO:0001587\|nonsense,SO:0001627\|intron_variant	SO:0001587\|nonsense,SO:0001627\|intron_variant
PDF	chr16	69364443	A	G	single_nucleotide_variant	Benign	not_provided	SO:0001583\|missense_variant,SO:0001627\|intron_variant	SO:0001583\|missense_variant,SO:0001627\|intron_variant

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
PDF	LUAD	chr16	69364026	69364028	GGG	-	In_Frame_Del	p.PL149del	3
PDF	LIHC	chr16	69363005	69363005	G	T	Missense_Mutation	p.H218N	2
PDF	HNSC	chr16	69363038	69363038	A	C	Missense_Mutation	p.W207G	2
PDF	PAAD	chr16	69364031	69364031	A	G	Missense_Mutation	p.F148S	1
PDF	SARC	chr16	69362967	69362967	G	T	Missense_Mutation		1
PDF	STAD	chr16	69364443	69364443	A	G	Missense_Mutation	p.W11R	1
PDF	BLCA	chr16	69362930	69362930	C	T	Missense_Mutation		1
PDF	BLCA	chr16	69362930	69362930	C	T	Missense_Mutation	p.D243N	1
PDF	HNSC	chr16	69362955	69362956	-	-	Frame_Shift_Ins		1
PDF	HNSC	chr16	69362955	69362956	-	G	Frame_Shift_Ins	p.K234fs	1
PDF	LIHC	chr16	69363005	69363005	G	T	Missense_Mutation		1

Copy number variation (CNV) of PDF
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across PDF
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
76597	COAD	TCGA-AA-3488-01A	RPL35	chr9	127623729	-	PDF	chr16	69363918	-

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
KIRP	PDF	0.000422540176066401	0.012
LUSC	PDF	0.00632422583020648	0.17
LUAD	PDF	0.0352638034673944	0.92

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LIHC	PDF	0.0397283004275426	1
LUSC	PDF	0.0236273841656158	0.71
THCA	PDF	7.24123529234471e-05	0.0024
KIRP	PDF	0.00945679413007471	0.29
LGG	PDF	0.000130508203311561	0.0042
LAML	PDF	0.0420624999434166	1
PAAD	PDF	0.0332376027643352	0.96
SKCM	PDF	0.0451585116204411	1

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
Q9HBH1	DB04310	2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide		Small molecule	Experimental
Q9HBH1	DB04368	Bb-3497	Inhibitor	Small molecule	Experimental
Q9HBH1	DB04310	2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide
Q9HBH1	DB04368	Bb-3497	Inhibitor

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID

Disease Name

# PubMeds

Disease source