# TSNE UMAP for each major region
annot['mr_tsne_coord']
# get palette
brain.get_sub_region_palette(region_type='CEMBA')
Try CEF test on ANOVA sig genes
Use 'region' category, and sig CEF means the gene is hypo in this region.
Search ISH data to see if the spatial pattern can be validated
a. Allen ISH database
b. Our MERFISH data
Papers
Scala, Federico, Dmitry Kobak, Matteo Bernabucci, Yves Bernaerts, Cathryn René Cadwell, Jesus Ramon Castro, Leonard Hartmanis, et al. 2020. “Phenotypic Variation of Transcriptomic Cell Types in Mouse Motor Cortex.” Nature, November. https://doi.org/10.1038/s41586-020-2907-3.
Gouwens, Nathan W., Staci A. Sorensen, Fahimeh Baftizadeh, Agata Budzillo, Brian R. Lee, Tim Jarsky, Lauren Alfiler, et al. 2020. “Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells.” Cell 183 (4): 935–53.e19.
O’Leary, Dennis D. M., Shen-Ju Chou, and Setsuko Sahara. 2007. “Area Patterning of the Mammalian Cortex.” Neuron 56 (2): 252–69.
About plotting, try major region coordinates
Try CEF test on ANOVA sig genes Use 'region' category, and sig CEF means the gene is hypo in this region.
Search ISH data to see if the spatial pattern can be validated a. Allen ISH database b. Our MERFISH data
Papers
Scala, Federico, Dmitry Kobak, Matteo Bernabucci, Yves Bernaerts, Cathryn René Cadwell, Jesus Ramon Castro, Leonard Hartmanis, et al. 2020. “Phenotypic Variation of Transcriptomic Cell Types in Mouse Motor Cortex.” Nature, November. https://doi.org/10.1038/s41586-020-2907-3. Gouwens, Nathan W., Staci A. Sorensen, Fahimeh Baftizadeh, Agata Budzillo, Brian R. Lee, Tim Jarsky, Lauren Alfiler, et al. 2020. “Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells.” Cell 183 (4): 935–53.e19. O’Leary, Dennis D. M., Shen-Ju Chou, and Setsuko Sahara. 2007. “Area Patterning of the Mammalian Cortex.” Neuron 56 (2): 252–69.