Download the extension to your home directory/GENE-E/extensions
RIGER-E may be downloaded and used free of charge by academic
and other non-profit
researchers. Commercial users please contact us
RIGER ranks shRNAs according to their differential effects between
two classes of samples, then identifies the genes targeted by the
shRNAs at the top of the list. In this way, RIGER identifies genes
essential to the difference between the classes. For details, see Luo, Cheung,
Subramanian, et al. (2008).
- The Class Comparisons parameter defines one or more class
comparisons on which to run RIGER. Click Edit to open the Edit
Comparison window. You can select columns by categories or by name.
For each class comparison, you select columns for the two classes to
be compared: Highlight the desired categories (or columns) in the
middle panel. Click an arrow icon to move them to class A or B. To
remove categories (or columns) from a class, highlight them and
click the delete icon. GENE-E moves them back to the middle panel.
- Optionally add another two class comparison by clicking the
- Select a method to analyze your RNAi screening data.
Second Best Rank
A method based on ranking genes
by the rank of the second best scoring hairpin for that gene. This is
currently the preferred method for RNAi screening analysis in the RNAi
A statistical method
and the basis for the original RIGER as described in Luo et al, PNAS,
This method is a modification of
the Second Best Rank in that it takes the combined sum of the first
and second best ranks for hairpins for a given gene. The best ranking
hairpin is given a weight of 0.25 and the second best ranking hairpin
is given a weight of 0.75. The sum of these weighted ranks is used to
compute a new score, and genes are ranked by this new score.
Regardless of the method you choose to use, you may use
either Signal to Noise or Log Fold Change to generate a single hairpin
level score from the set of replicates for each hairpin in your
screen. All the methods, including Kolmogorov-Smirnov, can use either
Signal to Noise or Log Fold Change. You may also use the T-Test
option, although this is still experimental and has not been fully
Please note that we now compute the FDR as
a p-value, and therefore additional permutations are required for the
When it is finished, RIGER
results are listed in the Navigator window as shown below.
Double-click the 'NES' or 'Scored shRNAs' to view the results.
Double-click 'Scored shRNAs' to
display a heat map showing the ranked list of shRNAs and their scores.
The heat map is sorted by the scores of the first comparison. Select
Tools>Sort Rows to sort a different comparison by score.
NES: Double-click 'NES' to display a heat map showing the
normalized enrichment scores (NES) for the genes in your dataset. The
heat map is sorted by the NES of the first comparison. Select
Tools>Sort Rows to sort a different comparison by the NES.
To view a report of RIGER results,
right-click either RIGER result node and select View Gene Report or
View Hairpin Report. To save the report, right-click either RIGER
result node and select Save Gene Report or Save Hairpin Report. The
report lists: Gene, Hairpins, # Hairpins, # Hairpins in the top 500,
1000, 5000, and 10000, NES, Gene rank, p-value, and p-value rank.