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PIIKA specifications

Information


Unique identifier OMICS_29172
Name PIIKA
Alternative name Platform for Intelligent, Integrated Kinome Analysis
Interface Web user interface
Restrictions to use None
Input data A file containing the intensity values for arrays.
Computer skills Basic
Version 2
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Brett Trost

Information


Unique identifier OMICS_29172
Name PIIKA
Alternative name Platform for Intelligent, Integrated Kinome Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Brett Trost

Publication for Platform for Intelligent, Integrated Kinome Analysis

PIIKA citations

 (8)
library_books

Differential Levels of Cecal Colonization by Salmonella Enteritidis in Chickens Triggers Distinct Immune Kinome Profiles

2017
PMCID: 5733560
PMID: 29322049
DOI: 10.3389/fvets.2017.00214

[…] iscovery rate; GO, gene ontology; IL, interleukin; JNK, c-Jun N-terminal kinase; KEGG, Kyoto Encyclopedia of Genes and Genomes; MAPK, mitogen-activated protein kinase; PBS, phosphate buffered saline; PIIKA2, Platform for Intelligent Integrated Kinome Analysis; PLCG1, Phospholipase C gamma 1; Pyk2, protein tyrosine kinase 2; qRT-PCR, quantitative real-time Reverse Transcriptase-PCR; S. Enteritidis, […]

library_books

Non digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota

2017
Microbiome
PMCID: 5635512
PMID: 29017607
DOI: 10.1186/s40168-017-0357-4

[…] r saturation levels, and averages of the nine intra-array technical replicates were used. Statistical testing, hierarchical clustering and coordinates for PCoA analysis were further processed through PIIKA2 (http://saphire.usask.ca/saphire/piika/), a web-based pipeline for kinome array processing []. […]

library_books

Molecular characterization of breast cancer cell lines through multiple omic approaches

2017
PMCID: 5460504
PMID: 28583138
DOI: 10.1186/s13058-017-0855-0

[…] sing local feature background intensity calculation with the default scanner saturation level.All data processing and analysis was done using the Platform for Intelligent, Integrated Kinome Analysis (PIIKA) software [], which is freely available for non-commercial use at http://saphire.usask.ca/saphire/piika. For each peptide within a given array, the chi-square test was performed to determine whe […]

library_books

Chicken Specific Kinome Array Reveals that Salmonella enterica Serovar Enteritidis Modulates Host Immune Signaling Pathways in the Cecum to Establish a Persistence Infection

2016
Int J Mol Sci
PMCID: 5000605
PMID: 27472318
DOI: 10.3390/ijms17081207

[…] Data normalization and PCA analysis was performed for both the peptide and antibody microarrays as per Li et al. [] using the PIIKA2 online platform (http://saphire.usask.ca/saphire/piika/index.html). Briefly, the array data were analyzed by subtracting the background intensity from the foreground intensity, variance stabili […]

library_books

Peptide Arrays for Kinome Analysis of Livestock Species

2014
PMCID: 4668848
PMID: 26664912
DOI: 10.3389/fvets.2014.00004

[…] While this remains a critical foundation of kinome analysis, there is also appreciation that this approach does not realize the full potential of information available within kinomic datasets.Through PIIKA 2, it is possible to define more discrete features of the kinomic data. For example, within an experiment, it is often possible to define sub-groupings based on a priori knowledge of biological […]

library_books

Identification of developmentally specific kinotypes and mechanisms of Varroa mite resistance through whole organism, kinome analysis of honeybee

2014
Front Genet
PMCID: 4033134
PMID: 24904639
DOI: 10.3389/fgene.2014.00139

[…] reatments were labeled “G4−” (susceptible and uninfested), “G4+” (susceptible and infested), “S88−” (resistant and uninfested), and “S88+” (resistant and infested). Kinome data were processed through PIIKA 2, a pipeline for processing kinome array data (Li et al., ; Trost et al., ), with the following study specifics. […]

Citations

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PIIKA institution(s)
Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada; Emerging Viral Pathogens Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA; Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
PIIKA funding source(s)
Supported in part by the Natural Sciences and Engineering Research Council of Canada (NSERC), Genome Canada, and the Intramural Research Program of the National Institutes of Health /National Institute of Allergy and Infectious Diseases.

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