Feb 06, 2024

Specificity index (pSI) calculation

DOI
https://dx.doi.org/10.17504/protocols.io.8epv5x8mjg1b/v1
  • 1University of Oxford
Peter Kilfeather
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DOI: https://dx.doi.org/10.17504/protocols.io.8epv5x8mjg1b/v1
Protocol Citation: Peter Kilfeather 2024. Specificity index (pSI) calculation . protocols.io https://dx.doi.org/10.17504/protocols.io.8epv5x8mjg1b/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 06, 2024
Last Modified: February 06, 2024
Protocol  Integer ID: 94805
Keywords: specificity index, psi, calculation from kilfeather, index, specificity, calculation
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
Specificity index (pSI) calculation from Kilfeather, Khoo et al., 2024
Protocol
To calculate the specificity index of genes detected within TRAP/RiboTag datasets of dopaminergic neurons and other cell types within midbrain, pSI (v1.1) was used with default settings22,24,38–40,73. Genes were considered significantly specifically expressed with an FDR-adjusted P value < 0.01.