ArticleBioinformatics (Oxford, England)2007
TAPPA: topological analysis of pathway phenotype association.
Article in Bioinformatics (Oxford, England), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Pathway metrics accurately stratify T cells to their cells states.BioData mining · 2024Article
- NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders.Nucleic acids research · 2024Article
- Review
- Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.Computational and structural biotechnology journal · 2021Article
- System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation.International journal of molecular sciences · 2020Article
- Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources.Metabolites · 2020Review
- Gene Set Analysis: Challenges, Opportunities, and Future Research.Frontiers in genetics · 2020Review
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- Single-cell technologies in reproductive immunology.American journal of reproductive immunology (New York, N.Y. : 1989) · 2019Review
- DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential Pathways.Genes · 2018Article
- Article
- Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data.Cell cycle (Georgetown, Tex.) · 2017Article
- Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes.BMC medical genomics · 2017Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- On the performance of de novo pathway enrichment.NPJ systems biology and applications · 2017Article
- ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.BMC bioinformatics · 2015Article
- Advanced Applications of RNA Sequencing and Challenges.Bioinformatics and biology insights · 2015Review
- A MATLAB tool for pathway enrichment using a topology-based pathway regulation score.BMC bioinformatics · 2014Article
- Methods and approaches in the topology-based analysis of biological pathways.Frontiers in physiology · 2013Review
- An inferential framework for biological network hypothesis tests.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Extracting biological insight from microarray data is important but challenging. Here we describe TAPPA, a java-based tool, for identification of phenotype-associated genetic pathways utilizing the pathway topological measures. This is achieved by first calculating a Pathway Connectivity Index (PCI) for each pathway, followed by evaluating its correlation to the phenotypic variation. Our PCI definition not only efficiently captures the contributions from genes that show subtle but consistent changes in expression, but also naturally overweighs the hub genes that interact with a large number of other genes in the pathway. TAPPA also allows evaluation of sub-modules within a pathway and their association to phenotypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.