ServerListAnalysis.pdf

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(Redirected from List Analysis)

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.

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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.

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  • 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.
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  • Step 1: Search: Search for a project on the server.
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  • 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.

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Step 3: Filter Projects

Projects can be filtered using the various meta data fields

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  • Advanced Options: Click this button to refine the list analysis.
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  • 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.


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Example Output

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.

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  • 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

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