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PEANuT specifications

Information


Unique identifier OMICS_25692
Name PEANuT
Alternative name Pathway Enrichment ANalysis Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Requirements
Cytoscape
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bianca H. Habermann

Additional information


https://sourceforge.net/p/peanut-cyto/wiki/Home/

Publication for Pathway Enrichment ANalysis Tool

PEANuT citations

 (10)
library_books

Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa

2018
Nat Commun
PMCID: 5945682
PMID: 29748556
DOI: 10.1038/s41467-018-04232-6

[…] their functions. The online software DAVID Bioinformatics Resources 6.8 was used to convert gene ID to ENTREZ_GENE_ID (https://david.ncifcrf.gov/content.jsp?file=functional_classification.html). The Pathway Enrichment Analysis tool Omicshare was used to classify genes at the level of KEGG_B_class (http://www.omicshare.com/tools/Home/Soft/pathwaygsea?l=en-us). Genes with significantly differential […]

library_books

Constitutively elevated levels of SOCS1 suppress innate responses in DF 1 immortalised chicken fibroblast cells

2017
Sci Rep
PMCID: 5727488
PMID: 29235573
DOI: 10.1038/s41598-017-17730-2

[…] cken microarray, as reported by Kong et al. after we had already obtained and processed our results.The resulting lists of differentially expressed transcripts were further analysed by the MetaCoreTM pathway enrichment analysis tool (Clarivate Analytics). The top 10 ranking canonical pathway maps associated with the upregulated transcripts in DF-1 cells are listed in Table . Upregulated transcript […]

library_books

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP Seq

2017
PLoS One
PMCID: 5513416
PMID: 28715427
DOI: 10.1371/journal.pone.0179141

[…] intron, and upstream 2k usually has different effects on gene expression. Therefore, we analyzed the biochemical pathways of all gene elements. We used the KAAS (KEGG Automatic Annotation Server) and pathway enrichment analysis tool of OmicShare software for all DMR-related gene elements to determine the functional pathways involved. According to the pathway enrichment analysis there were only 2 s […]

library_books

Human Pluripotent Stem Cell derived Cortical Neurons for High Throughput Medication Screening in Autism: A Proof of Concept Study in SHANK3 Haploinsufficiency Syndrome

2016
PMCID: 4972535
PMID: 27333044
DOI: 10.1016/j.ebiom.2016.05.032

[…] PA on SHANK3 mRNA. In parallel, RNA sequencing data indicated that lithium and VPA commonly up-regulated 12 genes while down-regulating 149 (c, ). This list of gene was further investigated using the pathway enrichment analysis tool PANTHER (Protein ANalysis THrough Evolutionary Relationships) via EnrichR. Commonly regulated genes did not cluster into signaling pathways linked to GSK-3 or any meta […]

library_books

Bisphenol A associated alterations in genome wide DNA methylation and gene expression patterns reveal sequence dependent and non monotonic effects in human fetal liver

2015
PMCID: 4922640
PMID: 27358748
DOI: 10.1093/eep/dvv006

[…] istance 3, both involved in the growth and maintenance of breast cancers. In addition, an enrichment analysis based on transcriptomic data from RNA-seq was performed using a logistic regression-based pathway enrichment analysis tool (LRpath) available at http://lrpath.ncibi.org. When enriched concepts among hypomethylated regions and over-expressed genes were compared, the metabolic and catabolic […]

library_books

A visual review of the interactome of LRRK2: Using deep curated molecular interaction data to represent biology

2015
Proteomics
PMCID: 4415485
PMID: 25648416
DOI: 10.1002/pmic.201400390

[…] In order to obtain a more global perspective on the putative interacting partners of LRRK2, we used the pathway-enrichment analysis tool offered by the annotated pathway database Reactome to highlight pathways in which human LRRK2 interacting partners are represented (). Term-enrichment analysis uses […]

Citations

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PEANuT institution(s)
CECAD Research Center, Cologne, Germany; Gregor Mendel Institute of Molecular Plant Biology, Austrian Acacdemy of Sciences, Vienna Biocenter (VBC), Vienna, Austria; Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Stuttgart, Germany; Research Group Computational Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
PEANuT funding source(s)
Supported by BMBF grant 315737 and 0315893B the Virtual Liver Network, SyBACol, the Robert Bosch Foundation, Stuttgart, Germany and the Max Planck Society.

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