analysis/01.SelectGenes/README.md

In PavlidisLab/neuroExpressoAnalysis: Marker genes of brain cell types and their use in analysis of whole tissue data

Marker gene changelog

Marker Genes

• Markers_1.2
• Markers_1.1
• Markers_1.0

Markers_1.2

This update fixes an issue with missing NCBI ids in the previous versions. It is also created using the latest gene annotations from Gemma, causing other minor changes.

For a complete list of genes added or removed from the "Combined" gene list see this file.

Below is the number of genes added or removed from all cell types across brain regions

| | added| removed| Total genes in final list| |:----------------------|-----:|-------:|-------------------------:| |Astrocyte | 26| 18| 428| |Ependymal | 1| 2| 68| |Microglia | 38| 38| 845| |Microglia_activation | 5| 7| 183| |Microglia_deactivation | 8| 13| 278| |Noradrenergic | 5| 1| 137| |Oligo | 21| 18| 438| |Purkinje | 1| 0| 49| |Pyramidal | 6| 1| 73| |ForebrainCholin | 1| 6| 103| |BrainstemCholin | 2| 0| 41| |Basket | 1| 0| 8| |CerebGranule | 1| 0| 13| |Golgi | 0| 1| 29| |GabaPV | 2| 0| 32| |Gluta | 1| 0| 11| |Endothelial | 8| 8| 191| |GabaRelnCalb | 1| 1| 24| |GabaVIPReln | 3| 2| 50| |OligoPrecursors | 7| 7| 211| |GabaSSTReln | 0| 2| 53| |SpinalCordCholinergic | 3| 1| 130| |Spiny | 1| 0| 75| |Dopaminergic | 2| 2| 60|

Markers_1.1

Edit: In May 2018, we have decided that the genes should be ordered the same way in both symbol files and NCBI id files. The NCBI id lists have been changed accordingly. Version number is not changed since the genes that are included are the same.

This update introduces minor fixes to the gene list due to the following factors

• A bug in the function that places samples into brain region. This resulted in oligodendrocytes isolated from the mouse neocortex to be added while selecting genes for cerebellar cell types even though we intended them to be not included since we had cerebellar oligodendrocyte samples.

• An update to the sample metada that changed which probes are selected to represent a gene during normalization. Probes selected for a 116 genes was effected due to this change. 16 new genes were included in the analysis due to the newly selected probe being above out selection threshold.

For a complete list of genes added or removed from the "Combined" gene list see this file.

Below is the number of genes added or removed from all cell types across brain regions

| | added| removed| Total genes in final list| |:----------------------|-----:|-------:|-------------------------:| |Astrocyte | 13| 19| 426| |Microglia | 37| 25| 844| |Microglia_activation | 6| 5| 187| |Microglia_deactivation | 12| 8| 279| |Noradrenergic | 2| 4| 135| |Oligo | 18| 9| 435| |ForebrainCholin | 4| 0| 106| |BrainstemCholin | 1| 1| 40| |Basket | 1| 1| 7| |Bergmann | 8| 2| 71| |CerebGranule | 0| 5| 12| |Golgi | 4| 1| 30| |Purkinje | 2| 1| 48| |DentateGranule | 1| 0| 22| |GabaPV | 0| 1| 30| |GabaRelnCalb | 1| 0| 24| |GabaVIPReln | 1| 0| 49| |GabaSSTReln | 1| 0| 55| |SpinalCordCholinergic | 1| 0| 128| |Spiny | 1| 2| 74| |Ependymal | 1| 0| 68| |Dopaminergic | 1| 2| 60|

Markers_1.0

Initial version submitted with paper

PavlidisLab/neuroExpressoAnalysis documentation built on Aug. 23, 2022, 7:42 a.m.