DARPA BioSPICE preApoptosis Use Case SEB effects on six timepoints data

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DARPA BioSPICE preApoptosisUse CaseSEB effects
on six time-points data

• Paolo BarbanoMarina SpivakMarco AntoniottiBud
  MishraNYU Bioinformatics Group

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Pre-Apoptosis 6 time points data analysis

• Six time-point data at 2h, 4h, 6h, 8h, 12h, 24h
• Cells treated with SEB
• Control untreated cells
• We used a straightforward k-means clustering to
  identify dominant features in expression patterns
  of experimental and control cells.
• We observed a global change in gene expression
  pattern in experimental cells relative to
  control the fluctuations in RNA levels that
  might be due to cell cycle become faster in the
  cells treated with SEB
• In the following we show three significant
  clusters that show these effects

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The second peak in gene expression in the cells
treated with SEB occurs sooner than in the
control
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The second peak in gene expression in the cells
treated with SEB occurs sooner than in the
control another example. The feature is present
in the majority of the examined genes.
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Clustering produces large groups with similar
expression patterns, indicating that the
acceleration in fluctuations is global and
synchronized
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Further Questions

• We cannot conclude yet whether the main damage
  caused by SEB is a result of aberrant
  transcription, protein-level action, or purely
  physical and mechanical effects (possibly
  influencing the cell cycle)
• From our analysis it is clear that SEB affects
  the transcription of the majority of the genes in
  the cell
• It still remains to determine whether there is a
  group of genes specifically affected by the
  signal transduction enzymatic cascade activated
  by SEB and what is their role in the overall
  changes occurring in the cell.