ArticleBMC bioinformatics2015
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.Nature communications · 2025Article
- Computational analyses of mechanism of action (MoA): data, methods and integration.RSC chemical biology · 2022Review
- ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research.Computational and structural biotechnology journal · 2021Article
- Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy.Frontiers in bioengineering and biotechnology · 2020Article
- Dynamically characterizing individual clinical change by the steady state of disease-associated pathway.BMC bioinformatics · 2019Article
- A comparative study of topology-based pathway enrichment analysis methods.BMC bioinformatics · 2019Article
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- Evidence for functional interactions between the placenta and brain in pregnant mice.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- Computational systems biology approaches for Parkinson's disease.Cell and tissue research · 2018Review
- Uterine influences on conceptus development in fertility-classified animals.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- How Can Synergism of Traditional Medicines Benefit from Network Pharmacology?Molecules (Basel, Switzerland) · 2017Review
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- Metabolomics and Integrative Omics for the Development of Thai Traditional Medicine.Frontiers in pharmacology · 2017Review
- Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPathway analysis methods, in which differentially expressed genes are mapped to databases of reference pathways and relative enrichment is assessed, help investigators to propose biologically relevant hypotheses. The last generation of pathway analysis methods takes into account the topological structure of a pathway, which helps to increase both specificity and sensitivity of the findings. Simultaneously, the RNA-Seq technology is gaining popularity and becomes widely used for gene expression profiling. Unfortunately, majority of topological pathway analysis methods remains without implementation and if an implementation exists, it is limited in various factors.
resultsWe developed a new R/Bioconductor package ToPASeq offering uniform interface to seven distinct topology-based pathway analysis methods, of which three we implemented de-novo and four were adjusted from existing implementations. Apart this, ToPASeq offers a set of tailored visualization functions and functions for importing and manipulating pathways and their topologies, facilitating the application of the methods on different species. The package can be used to compare the differential expression of pathways between two conditions on both gene expression microarray and RNA-Seq data. The package is written in R and is available from Bioconductor 3.2 using AGPL-3 license.
conclusionToPASeq is a novel package that offers seven distinct methods for topology-based pathway analysis, which are easily applicable on microarray as well as RNA-Seq data, both in human and other species. At the same time, it provides specific tools for visualization of the results.
Indexed as
Identifiers
What OpenQuestion holds
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.