Enrichr help - what do "up" and "down" lists refer to?
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5.9 years ago
rakrasnoff • 0

Hi there,

I was hoping for some help interpreting the Enrichr output. When I give Enrichr a list of genes, not specifying any enrichment values or "membership levels", the output gives me options such as "Allen brain atlas up", or "Allen brain atlas down". I've done some reading, but haven't been able to figure out what exactly the "up" and "down" refer to. I assume it has something to do with up/down regulation of expression? But I wasn't sure how the system was making these inferences, given that I have not given it any enrichment information.

Any help would be very much appreciated! Thank you!!

screen shot of output https://s32.postimg.org/c3npj5b5h/Screen_Shot_2016_07_22_at_10_02_29_AM.png

RNA-Seq • 2.0k views
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5.9 years ago
venu 7.0k

Did you look at Enirchr publication ? (Explained in supplementary data here)

Allen Brain Atlas application programming interface (API) to download normalized gene expression values for 20,000 genes measured in 2,500 distinct brain regions. We filtered the data matrix to remove genes and brain regions with more than 5% missing values, imputed the remaining missing values, and log2-transformed all values. We then standardized the values for each gene to obtain scores indicating the significance of up- or down-regulation of each gene relative to its median. Finally, we created gene set libraries with brain regions labeling the 300 most up- or down-regulated genes relative to their median expression in the brain.

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Thank you so much! I completely missed that!

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