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hPDI specifications

Information


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 in publications

 (7)
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] 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 […]

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

[…] of genomic intervals was assessed using bedtools., 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. […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 4060870
PMID: 24885462
DOI: 10.1186/1755-8794-7-27

[…] represented the experimentally-determined binding preference of a human tf or dna-binding protein. motifs were obtained by pooling collections from five sources (i.e., jaspar, uniprobe, encode, hpdi and transfac) [-], as described in a recent publication []. to identify motif matches in the human genome, intergenic sequences were scanned with masking of repetitive dna elements and assembly […]


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

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