List analysis is a server-based analysis that allows a user to search projects by a user-uploaded list of identifiers (e.g. gene symbols). Given this list of identifiers, this analysis will search over projects and rank the studies based on the “relevance” to the input symbols.
Input Data Requirements
A list of IDs (e.g. genes or SNP IDs) users would like to perform List Analysis on.
Step 1: Choose Input Type
The user has to first select the type of input.
- This could be either a list of ID's, or the user can create a list from an existing project on the server.
- The type of ID's must also be specified. The options are Master ID's and Row names.
- If the user chooses to create a list from an existing project on the server, the Get List From Server Project wizard will be presented.
- Step 1: Search: Search for a project on the server.
- Step 2: Create a list from: Choose the inference report to create a list from. Users can further filter by raw p-value, fold change or Max(LSMean).
- Step 3: Get List From Server: Click this button will generate the list of IDs that satisfy the above criteria.
Step 2: Input List
The user must input or paste the symbols for ID's into the text box. Alternatively, Load from file , Load from server and Load from solution options are also available to input the symbols.
- Load from solution requires the project to be open in the Server tab.
- Translate IDs Users can translate a list of IDs to another list of IDs based on an ID translation managed by the administrator.
Step 3: Filter Projects
Projects can be filtered using the various meta data fields
- Advanced Options: Click this button to refine the list analysis.
- Fetch top: Only show the top results, sorted by P value.
- Minimal match: the minimum number of matched/overlapped IDs between the provided list and the target inference report.
- Significance levels: Users can provide multiple significance levels separated by ",". The final analysis report will be divided by the significance levels (see the output below).
- Filter by fold changes: Users can filter the target inference report by fold changes.
- Filter by Max(LSMean): Users can filter the target inference report by Max(LSMean).
Step 4: Finish
Once all information is entered, the window will indicate that all information has been collected. Click Finish.
The completed analysis will present a new ListAnalysis tab, containing a ListAnalysis Table and a ListAnalysis Report. A Fisher Exact test is performed by matching the user-provided list to the inference reports in server projects.
- Fisher PValue: Fisher raw p-value
- SigMatched: Significant genes matched by the list
- Sig: Significant genes
- Matched: Genes in the inference report matched by the list
- Counts: Count number
- Up%: Percentage of upregulated genes
- Down%: Percentage of downregulated genes