Related Experiment Video
Updated: Jun 1, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
TAFFEL: Independent Enrichment Analysis of gene sets
Mitja I Kurki1, Jussi Paananen, Markus Storvik
1Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
Background:
A major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, controlled by distinct regulatory mechanisms. Many of these pathways and the associated regulatory mechanisms might be obscured by a large number of other significant processes and thus not identified as significant by standard gene set enrichment analysis tools.
Results:
We present a novel method called Independent Enrichment Analysis (IEA) and software TAFFEL that eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators. IEA indicates transcriptional regulators putatively controlling biological functions in studied condition.
Conclusions:
We demonstrate that the developed method and TAFFEL tool give new insight to the analysis of differentially expressed genes and can generate novel hypotheses. Our comparison to other popular methods showed that the IEA method implemented in TAFFEL can find important biological phenomena, which are not reported by other methods.
Related Concept Videos
Friedman Two-way Analysis of Variance by Ranks
Law of Independent Assortment
Law of Independent Assortment
Combinatorial Gene Control
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
DNA Microarrays
Extraction: Partition and Distribution Coefficients
For extracting a solute from an aqueous phase into an organic...

