BrainSpan gene expression analysis

[Priyadarshini Thirunavukkarasu]

Hello

I used the BrainSpan atlas dataset to analyse how the genes in my input list are differentially regulated. I could see the output file showing which are the genes upregulated or downregulated at each developmental time point. But, I couldn't find the information in which brain region these genes are upregulated or downregulated. So, if a gene is shown upregulated , does it mean it is upregulated in all the brain regions at given developmental time point compared to other time points?. If two genes are shown to be differentially upregulated, does it mean the genes are coexpressed?.

Thanks

Priya

[Marijn Schipper]

Hi Priya,

In this dataset, the RNA-seq samples from the whole brain is pooled. 
So, if a gene is shown upregulated , it could be upregulated everywhere in the brain or strongly upregulated in a specific region. 

If you know the gene and the timepoint, you could look in the original dataset (http://www.brainspan.org/api/v2/well_known_file_download/267666529) where the data is not yet pooled to see in which brain regions this effect manifests.
We indeed defined differential expression as timepoint vs average of other timepoints. 
If you would like more co-expression information on genes in the developing brain, I would suggest you check out the original publication where a co-expression analysis is performed. (https://www.nature.com/articles/nature13185).
Please let me know if this does not fully answer your questions.

Cheers,

Marijn

Op zondag 9 oktober 2022 om 20:15:10 UTC+2 schreef priy...@gmail.com: