RNAiCut User Guide



1. Input a list of CG gene names, ranked in decreasing order from increasing to decreasing absolute value of score. We recommend limiting the list to 4,000 genes so that the program can run quickly.

Example: If one wanted to find the cutoff for the following list of genes with their corresponding scores:

CG33894 1.23
CG6474 2.45
CG3845 3.67
CG4699 0.89
CG8053 1.98
CG9696 2.76
CG3412 0.54

one would input:

CG3845
CG9696
CG6474
CG8053
CG33894
CG4699
CG3412

Another Example: If one wanted to find the cutoff for the following list of genes with their corresponding scores:

CG40461 -1.45
CG11195 -2.67
CG12821 -3.98
CG2637 -0.54
CG17358 -1.76
CG11132 -2.98
CG4019 -0.23

one would input:

CG12821
CG11132
CG11195
CG17358
CG40461
CG2637
CG4109

If you would like to do local scrambling, input genes and scores, with a tab separating each gene and its corresponding score. In this case, the order of the genes does not matter.

Local scrambling example: If one wanted to find the cutoff for the following list of genes with their corresponding scores:

CG33894 1.23
CG6474 2.45
CG3845 3.67
CG4699 0.89
CG8053 1.98
CG9696 2.76
CG3412 0.54

one would input:

CG33894 1.23
CG6474 2.45
CG3845 3.67
CG4699 0.89
CG8053 1.98
CG9696 2.76
CG3412 0.54

2. If you are doing local scrambing, check the "Do local scrambling" box, and type in the "Local scrambling range" box the range of z-scores for genes that you would like to randomly re-order. In our study, we evalutated robustness by randomly re-ordering genes within a 0.05 z-score range, so we would have typed "0.05" in the box.

3. RNAiCut will do local scrambling if you checked the "Do local scrambling box" and find the cutoff for your list.

4. RNAiCut will give you the following information (c and d are included when local scrambling is not done):

a. Plot

b. Location of global minimum on plot

c. Location of gene at plot's global minimum in the list you inputted

d. Link to a list of the significant genes (genes earlier than and including cutoff)

e. Link to a list of genes, in ranked order (with repeats removed), and the logs of their corresponding p-values.