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Data interpretation #5
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Hello @Domikohlh, The shift to the left for siRNA target genes (or miRNA target genes) would imply that those genes are potentially targeted by the siRNA. The D statistic reported is the maximum difference between the background distribution and the target gene distribution. Our null hypothesis is that there should be no difference between the distribution of those sets of genes. The p-value is generated from the KS test. Here are some documents that might help. Feel free to post more questions and I will try to help! The literature has used ECDFs to gauge siRNA off target effects. This package and article cite the following example: https://academic.oup.com/nar/article/50/12/6656/6613918 ECDF overview: https://www.library.virginia.edu/data/articles/understanding-empirical-cumulative-distribution-functions |
Hi @tacazares, This is absolutely fine. I’m sorry that I typed that wrong. That should be single-cell RNA sequencing, not siRNA-seq. I know scRNA-seq will have a slightly more info than the bulky one so it’s just to make sure that the gene expression profile generated by both single-cell and bulky would be the same. I will take a look of the paper. Thanks a lot! |
It is a great idea to perform a scRNA-seq to siRNA knockdown samples. It will be exciting to see data public data and check what it looks like for siRNA knock-down assay. |
Hi,
I have a few questions about the software.
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