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Related Experiment Video

Updated: Dec 23, 2025

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
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SPEED2: inferring upstream pathway activity from differential gene expression.

Mattias Rydenfelt1,2, Bertram Klinger1,2, Martina Klünemann1,2

  • 1Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin 10117, Germany.

Nucleic Acids Research
|April 22, 2020
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Summary
This summary is machine-generated.

The SPEED2 web server provides updated signalling pathway signatures from extensive transcriptome data. It helps identify pathway dysregulation in diseases by analyzing gene expression patterns.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Inferring mechanistic origins of transcriptomic dysregulation, particularly in disease, is crucial.
  • Enrichment analysis of signature genes in differentially regulated genes is a common method for pathway activity inference.
  • The previous SPEED database offered signatures for signalling pathways derived from public transcriptome data.

Purpose of the Study:

  • To present a substantial upgrade to the SPEED database, named SPEED2.
  • To provide an updated web server hosting consensus signatures for 16 signalling pathways.
  • To introduce a new method for deriving and scoring 'continuous' gene signatures.

Main Methods:

  • Integration of a large number of transcriptomic signalling perturbation experiments.
  • Development of consensus signatures for 16 signalling pathways.
  • Derivation of 'continuous' gene signatures using a transparent and automated algorithm without fine-tuning.

Main Results:

  • SPEED2 offers updated and refined signatures for 16 key signalling pathways.
  • The web server enables inference of deregulated signalling pathways from user-provided gene lists (e.g., differentially expressed genes).
  • A novel algorithm for scoring continuous gene signatures has been developed and described.

Conclusions:

  • SPEED2 represents a significant advancement in tools for analysing signalling pathway activity from transcriptome data.
  • The enhanced signatures and new scoring algorithm facilitate more accurate and automated inference of pathway dysregulation.
  • This resource aids in understanding the mechanistic basis of transcriptomic changes in biological contexts, including disease.