Table of Contents

Tutorial

Scenario

The final aim of a typical genomic experiment is to find a molecular explanation for a given macroscopic observation. The common scenario is based on the comparison of expression patterns between different groups (i.e. control and disease, time series experiments, etc.) which results in a group genes of interest either because they co-express in a cluster or because they are significantly over- or under-expressed when two classes of experiments are compared. The deregulated list of genes can easily grow up to one hundred. Logically, one could conclude that there are not hundreds of errors (mutations, deregulation, etc.) but one (or a few) common cause leading to the abnormal expression of these genes. Regulatory elements, which generally interact and regulate several genes, are features of interest because of its potential to cause this deregulated profile.

Getting started

To start using RENATO clik on the Enrichment analysis link at the top left of the screen and automatically you will redirected to the form page.

 Enter form

  1. Upload your data: go to the Upload data button and upload your files or text. See Upload your data section to find details on how to upload your data. For information on the input file formats see Input file formats section.
  2. Select the specie you are going to work with. We currently support analyses for human and mouse, but soon new species will be added.
  3. Functional analysis: Depending on you input file, you can run either a Single enrichment analysis or Gene set analysis. If your input file is an unordered gene list select the FatiGO option, however, to analyze ordered gene lists chose between Fatiscan and Logistic model. Please, visit the Functional analysis section to see detailed information about each particular method.
  4. Select your file: By clicking on *_Browse file_* you will be able to select among the uploaded files.
    Browse file
    Select file
  5. Select a database: Select whether you want to analyse your genes for TFBSs or miRNAs.
    - TFBS (Transcription Factor Binding Site): This option will test if there is a common transcription factor for your gene list.
    - miRNA: This option will test if there is a common microRNA for your gene list.
    Alternatively, you can upload your own annotation: users who are working on species that our database does not support or that want to use their own annotation can upload them using the Upload data menu using the format described here.
  6. Run: Once all options are set you can run the job. You may get some error message if some parameters are not properly set. Insert a name for this job and click Run. The job will appear at the Jobs and Data list panel. Wait until the job is colored green to click and check your results.
tutorial.txt · Last modified: 2012/04/23 18:55 by mbleda
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