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hPDI specifications


Unique identifier OMICS_03024
Name hPDI
Alternative name Human Protein-DNA Interactome
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Human Protein-DNA Interactome

hPDI citations


Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

BMC Genomics
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] 19&g=wgEncodeAwgTfbsUniform) were utilized.To identify transcription factor binding sites (TFBS) from the DNase-DGF data, TRANSFAC (2013.2), JASPAR (2010), UniPROBE, BEEML-PBM, high-throughput SELEX, Human Protein-DNA Interactome, and transcription factor binding sequences of ENCODE ChIP-seq data were used [–]. Position weight matrices of transcription factor binding sequences were transformed int […]


Constructing 3D interaction maps from 1D epigenomes

Nat Commun
PMCID: 4792925
PMID: 26960733
DOI: 10.1038/ncomms10812

[…] , and Wilcoxon test was used to compute P values.For motif-enrichment analysis, a library of 292 non-redundant motifs were assembled by combining the DNA binding motifs in Transfac, Jaspar, Uniprobe, hPDI and Taipale. A PWM scan was performed in each hotspot and non-hotspot region and a motif score was computed. A threshold of 0.6 was used to determine the presence or absence of a motif. The numbe […]


Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells

PLoS One
PMCID: 4658012
PMID: 26599758
DOI: 10.1371/journal.pone.0143627

[…] tors.To define a wide collection of human PWMs we used the Bioconductor Package MotifDB ([]), that collects TF binding preference information from several sources (among which Jaspar [], UniPROBE [], hPDI [] and Ref. []). We were able to retrieve 1298 matrices associated with a human Entrez ID. Shuffled PWMs were obtained by randomly permuting the positions, thus maintaining the base composition o […]


Deciphering H3K4me3 broad domains associated with gene regulatory networks and conserved epigenomic landscapes in the human brain

PMCID: 5068762
PMID: 26575220
DOI: 10.1038/tp.2015.169

[…] For motif analyses, including enrichment and comparative matching of de novo sequences, five databases were combined, Transfac, Jaspar, Uniprobe, hPDI and Taipale. De novo motifs were compared against a total of 3764 motifs by EPIGRAM using k-mer features with lasso regularization to characterize motifs associated with H3K4me3 in NeuN+ nuclei. […]


Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites

PMCID: 4392043
PMID: 25883770
DOI: 10.1186/s40169-015-0054-5

[…] ng affinities of human and/or mouse TFs and uDBPs. The 2935 motifs were selected from an initial set of 4378 motifs pooled from multiple sources, including the human protein-DNA interaction database (hPDI) [], Jaspar [], UniPROBE [] and TRANSFAC Professional (release 2013.4) [] (Additional file ). We also included motifs derived from a recent analysis of ENCODE ChIP-Seq datasets [,], as well as on […]


Genomic mapping of the MHC transactivator CIITA using an integrated ChIP seq and genetical genomics approach

Genome Biol
PMCID: 4243378
PMID: 25366989
DOI: 10.1186/s13059-014-0494-z

[…] elected. The tool Biostrings 2.32.1 from the BioConductor Package was used to scan for presence of RFX5, CREB and NF-Y motifs (source for PWM-Position Weight Matrices used: JASPAR [], Transfac [] and Human Protein-DNA Interactome (hPDI) []) and score similarity of any motif identified within a segment against the PWM in question. This was carried out iteratively within a segment to obtain a CIITA […]

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hPDI institution(s)
Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

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