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Gene Expression

Purpose:

  • inspect expression trajectories for selected genes across datapoints
  • compare one or multiple genes in the same view

Inputs:

  • one loaded dataset
  • one or more selected genes
  • selected transformation scale

Available transformations:

  • Proteomics/phosphoproteomics: continuous, log-scale, total intensity, median normalization
  • RNA-seq: continuous, log-scale, TPM, FPKM, TMM, CPM

How to use:

  1. Open Gene Expression.
  2. Search and select one or more genes.
  3. Choose transformation/scale.
  4. Inspect line/trend behavior across stages.

Outputs:

  • gene-level trend plot
  • corresponding table output for selected view

Practical tips:

  • For phosphoproteomics, one gene may produce multiple peptide trends.
  • Validate stage ordering and replicate naming in your input columns.
  • Compare transformed and continuous views before conclusions.

Gene Expression module with selected protein trends

Figure 4. Gene Expression view for selected proteins across stages. Individual points show replicate-level values, and the connected markers summarize the stage-wise trend for each selected feature.

Help: how to read this plot

Use this view to inspect candidate-level behavior after broader analyses such as PCA, heatmaps, or volcano plots. A convincing pattern usually combines a coherent trend across stages with reasonable replicate agreement. For phosphoproteomics, one gene can produce multiple peptide-level trends, so separate lines may represent related but distinct measurements.