Feb 07, 2024
Specificity index (pSI) calculation
- 1University of Oxford
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 07, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94805
Funders Acknowledgement:
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
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.