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v1.12.0: protein-level test in an independent spinal-cord proteome (Amendment 17, W75)

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@guokai8 guokai8 released this 15 Oct 04:03
v1.12.0
d6f4193

This is the release cited by the submitted manuscript.

New: W75, protein-level test (Amendment 17)

scripts/run_w75_spinal_cord_proteome.R and docs/analyses/W75_spinal_cord_proteome.md test the ALS-up module proteins in an independent human spinal-cord proteome.

  • Data: PRIDE PXD067060 (Feneberg et al. 2025; Oxford Brain Bank), detergent-soluble fraction. 14 ALS, 7 control, 6 PD and 9 AD donors.
  • Specification: the analysis was specified and committed before any expression value was read.
  • ALS vs control:
    • ANXA1: log2FC 1.84, FDR = 0.002.
    • C3: log2FC 1.63, FDR = 0.043.
    • GPNMB: log2FC 1.00, P = 0.39. Higher in direction, but quantified in only 14 of 21 samples.
  • Module set test: could not be computed, because only 1 of the 3 quantified proteins was measured in every sample (deviation recorded in S3).
  • Other diseases: GPNMB separated ALS from PD (P = 0.002). ANXA1 was also raised in PD and AD.

Supplementary Tables

  • S1: Amendment 17 added.
  • S2: 15 W75 rows added.
  • S3: two W75 deviations added.
  • S4t (new): module-protein results.

README

The README adds the data source, the source-data layout and pipeline step 12i.

Assets 2
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