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TAPPA specifications


Unique identifier OMICS_19190
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability No
Maintained No


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TAPPA citations


A critical comparison of topology based pathway analysis methods

PMCID: 5784953
PMID: 29370226
DOI: 10.1371/journal.pone.0191154

[…] seven representative methods identifying differentially expressed pathways between two groups of interest based on gene expression data with prior knowledge of pathway topologies: spia, prs, cepa, tappa, topologygsa, clipper and degraph. we performed a number of controlled experiments that investigated their sensitivity to sample and pathway size, threshold-based filtering of differentially […]


Advanced Applications of RNA Sequencing and Challenges

PMCID: 4648566
PMID: 26609224
DOI: 10.4137/BBI.S28991

[…] and the interactions of the genes in the pathway are considered. accordingly, interacting differentially expressed gene pairs are preferentially weighted over two non-interacting genes. similarly, tappa is a scoring method in which higher weights are automatically assigned to hub genes and interacting gene pairs. deap identifies the most differentially expressed path to provide a refined focus […]


Methods and approaches in the topology based analysis of biological pathways

PMCID: 3794382
PMID: 24133454
DOI: 10.3389/fphys.2013.00278

[…] this issue while still using all gene measurements uses the individual p-values of each gene (voichiţa et al., )., among the surveyed methods, scorepage, pathologist, netgsa, topologygsa, pwea, tappa, acst, bpa, bapa-iggfd, and degraph use all genes together with their expression values as input. however, for bpa and bapa-iggfd, the fold changes are only used to label each gene […]


Identification of highly synchronized subnetworks from gene expression data

PMCID: 3698028
PMID: 23901792
DOI: 10.1186/1471-2105-14-S9-S5

[…] properties of its interaction networks. its advantages have been demonstrated []. this metric was later implemented in a software tool entitled topological analysis of pathway-phenotype association (tappa). here to capture contributions from topological characteristics of the dynamic interaction network, we integrate the phase locking analysis into pci to define a novel metric: […]

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TAPPA institution(s)
The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, USA
TAPPA funding source(s)
Supported by the National Institute of Diabetes and Digestive and Kidney Diseases under grant No. R01DK080100.

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