PinnacleZ specifications

Information


Unique identifier OMICS_08333
Name PinnacleZ
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
Version 1.1
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Publication for PinnacleZ

PinnacleZ in publications

 (6)
PMCID: 5662748
PMID: 29085035
DOI: 10.1038/s41598-017-14682-5

[…] is compared with support vector machine-recursive feature elimination, multivariate empirical bayes statistics, analyzing time-series data based on dynamic networks, molecular networks based on pcc, pinnaclez, graph-based iterative group analysis, keypathwayminer and bionet. the better performance of pb-dsn not only demonstrates its effectiveness for the identification of discriminative features […]

PMCID: 5335754
PMID: 28253853
DOI: 10.1186/s12859-017-1567-2

[…] practical performance of each method. using both simulation studies and a real data application, we evaluated the performance of different methods in terms of recall and precision., jactivemodules, pinnaclez and wmaxc performed well in identifying subnetwork with relative high precision and recall. bionet performed very well only in precision. as none of methods outperformed other methods […]

PMCID: 5445589
PMID: 28649433
DOI: 10.1038/s41540-017-0007-2

[…] the results for the i2d network are depicted in supplementary figsĀ  and ., we can further categorize tools based on the characteristic of their internal parameters (ip). cosine, giga, gxna, and pinnaclez restrict the solution to a user-specified size. in contrast, bionet, degas and kpm allow for noise (exceptions or outliers) in the reported solutions, such that sub-networks […]

PMCID: 3870302
PMID: 24391662
DOI: 10.3389/fgene.2013.00289

[…] the significance with respect to the local and global null distribution of the activity scores and with respect to the null distribution of mutual information scores. we used the java package pinnaclez as an implementation of the algorithm. pinnaclez performs a z-normalization prior to the subnetwork search, which is depreciated in a fivefold cross validation. therefore, we implemented […]

PMCID: 3727179
PMID: 23956970
DOI: 10.1155/2013/210253

[…] or complex. since genes function in collaboration rather than alone, subnetworks are more rational than independent responsive genes, from a biological perspective []., in this study, we used pinnaclez algorithm [] to integrate microarray and ppi data. in addition to pinnaclez algorithm, there are several other studies which provide different ways to integrate gene-expression data […]


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PinnacleZ institution(s)
Bioinformatics Program, University of California San Diego, La Jolla, CA, USA

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