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Protocols

PAPST specifications

Information


Unique identifier OMICS_08501
Name PAPST
Alternative name Peak Assignment and Profile Search Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Hong-Wei Sun

Publication for Peak Assignment and Profile Search Tool

PAPST citations

 (6)
library_books

Ion and metabolite transport in the chloroplast of algae: lessons from land plants

2018
PMCID: 5948301
PMID: 29541792
DOI: 10.1007/s00018-018-2793-0

[…] ht stress in A. thaliana [, ]. TAAC was also localized to the envelope and found to use additional substrates such as phosphoadenosine 5′ phosphosulfate []. The envelope-localized protein is known as PAPST1, and is proposed to play role in sulfur metabolism, including the biosynthesis of thiols, glucosinolates, and phytosulfokines. Phylogenetic analyses revealed TAAC/PAPST1 homologues in green alg […]

library_books

Subset and tissue defined STAT5 thresholds control homeostasis and function of innate lymphoid cells

2017
PMCID: 5626390
PMID: 28916644
DOI: 10.1084/jem.20150907

[…] of IL-15 (P < 0.05). Only genes with mean RPKM > 2 in either ex vivo or IL-15–treated NK cells are included (Table S4).Direct comparison of peak distribution across experimental groups was done with PAPST and annotated to the nearest gene using HOMER. Peaks are assigned to genes if they occur within introns, exons, and/or <50 kb from transcriptional start sites. Peak distribution was further anal […]

call_split

Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease

2017
Sci Rep
PMCID: 5524929
PMID: 28740121
DOI: 10.1038/s41598-017-06539-8
call_split See protocol

[…] e in the Galaxy and/or Galaxy/Cistrome platforms (https://usegalaxy.org/; http://cistrome.org/ap/root). In combination with BETA minus, we also used PAVIS (http://manticore.niehs.nih.gov/pavis2/) and PAPST tools, (https://github.com/paulbible/papst) to select and prioritize the candidate DNMT3b target genes.Two different analyses were used to obtain a feasible and reliable number of Dnmt3b target […]

call_split

A novel DLX3–PKC integrated signaling network drives keratinocyte differentiation

2017
Cell Death Differ
PMCID: 5384032
PMID: 28186503
DOI: 10.1038/cdd.2017.5
call_split See protocol

[…] he DNA Library was prepared after fragment purifications and sequenced using Illumina HiSeq 2000 (Illumina, San Diego, CA, USA). MACS 1.4 was used for peak calling and Integrative Genomics Viewer and PAPST was used to visualize the peak regions from Transcription Start Sites (TSS). […]

call_split

HIRA Is Required for Heart Development and Directly Regulates Tnni2 and Tnnt3

2016
PLoS One
PMCID: 4982693
PMID: 27518902
DOI: 10.1371/journal.pone.0161096
call_split See protocol

[…] using RPKM. Lists of genes within +/- 5Kb of the TSS and TES was generated using Strand NGS. Bedtools intersect tool was used to define the overlapping peaks between different BED files. In addition, PAPST (Peak Assignment and Profile Search Tool) software was used to overlap regions of interest and establish genome wide enrichment patterns of HIRA ChIPseq []. […]

library_books

Signal transducer and activator of transcription 5 (STAT5) paralog dose governs T cell effector and regulatory functions

2016
eLife
PMCID: 4856466
PMID: 26999798
DOI: 10.7554/eLife.08384.034

[…] percentage of peaks found within 10 kb intervals of the nearest transcriptional start sites and plotted as histograms. Direct comparison between experimental groups (i.e. peak overlap) was done with PAPST (). Circos plot was generated by inputing the number of shared peaks between experimental groups to the Circos Table Viewer (http://mkweb.bcgsc.ca/tableviewer)(). Violin plot was generated by in […]

Citations

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PAPST institution(s)
Biodata Mining and Discovery Section, Office of Science and Technology, Intramural Research Program, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA

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