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Marmite input

Online examples

Here you can load small datasets from our server. You can use them to run examples and see how the tool works. Click on the links to load the data.

  • Example 1: marmite demo1 A list of human genes related to neoplasm. Run the example with the default options.

Select your data

Your data must be two lists of human gene identifiers as an idlist data type, the list2 generally the background set. The annotations were created using HUGO ids. Then Marmite converts any gene identifier to HUGO id through an ensembl id, if you provide gene names the conversion process will be omitted.

Bio-entity name

Users can evaluate their genes using three categories of bio-entities:

  • disease associated words
  • chemical products
  • word roots.

Filter bio-entities

  • Minimum number of genes with a score Select minimum number of genes with a score for an entity. Entities with less than this number in both lists will be excluded from the analysis. Minimum default is set to 5.
  • Number of bio-entities in results Select the number of bio-entities showed in the results page. A normal analysis may evaluate about 200-300 words depending on lists and gene relevance. The output can be extra informative or even too big to display if we showed all bio-entities evaluated. Therefore, Marmite permits the restriction of the output to 50 bio-entities set as default.

Job

  • Job name. Give a short name to your analysis job
  • Job description. You can use this section to document further the characteristics of this analysis

Its aim is to help you identifying the analysis you are running and distinguishing between several analysis.
To set the name is mandatory but you can leave the description empty if you do not want to use it.

Run

Once all options are set you can run the job. You may get some error message if some parameters are not properly set. If you do, just check the options you have chosen.

See Methods section for details on the algorithms.
See Output results section for details on the result data format and plots.