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Eva Alloza, 05/31/2010 04:41 pm

Home >> Functional profiling documentation

Marmite output


In this section you will find a reminder of the two lists analysed that can be downloaded as a text file. Also the two correspondent files to the excluded entities due to the filtering applied to each of the uploaded lists.


In this section you will find a table containing the found entities after applying the Kolmogorov-Smirnov test to the input lists. In addition, for each entity Marmite returns its corresponding statistic, p-value and adjusted p-value. The table is sorted by the adjusted pvalue but can be sorted up and down by another column by just clicking in its column headings. In the bottom of the table the user can move within the various pages which the table has been broken down. The information contained in the table corresponds to:

  • entities: the bio-entity tested, you can follow the link to general databases as Ensembl or novo|seek
  • statistic: score calculated by the Kolmogorov-Smirnov test
  • side:
  • box-plot:
  • pvalue: unadjusted pvalue from the Kolmogorov-Smirnov test
  • adj pvalue: adjusted pvalue from the Kolmogorov-Smirnov test, after correcting for multiple testing, using the FDR procedure of Benjamini & Hochberg. Keep in mind to use this pvalue instead of the unadjusted one as Marmite is performing a great number of test simultaneously and the error rate must be corrected.
  • genes (list 1): list of genes co-occurrent with this bio-entity in list 1
  • genes (list 2): list of genes co-occurrent with this bio-entity in list 2

Other actions

  • Open input form: Marmite opens the input form with the same parameters that the user used for this experiment before. It is a feature to permit the re-running of the same experiment but varying some of the parameters of the experiment.