How to rank genes based on differential expression experiments?

Thousands of differential expression experiments are available in the platform. Genes in a set can be ranked based on these experiments to determine whether a gene is differentially expressed for a disease, phenotype, or compound.

ranking_for_DE

Steps

Note:

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1. Create or open an Analytic project and select genes of interest in the [Data Selection] section. The ranking analysis works best for genes.

2. Scroll down to the [Method Selection] section.

3. Click on the [Ranking Selection] tab to select the criteria for the genes ranking.

rank_selection_main_page4. Click on the [information icon] to get a description of the ranking criteria.

5. Click the box next to [Differential expression] to make the selection.

Note: The [Classification] ranking option is selected by default. 

6. The [Differential Expression Score] window appears with three categories for selection:

  • To determine whether a gene is differentially expressed in a disease: select [Disorders] and type in the name of the disease in the [Search for concept] text box. Select the term that best matches your input.
    disorders_DE_ranking
  • To determine whether a gene is differentially expressed after treatment with a compound: select [Chemicals & Drugs] and type in the name of the compound in the [Search for concept] text box. Select the term that best matches your input.
    chemical_drugs_DE_ranking
  • To determine whether a gene is differentially expressed in a phenotype: select [Physiology]  and type in the name of the phenotype in the [Search for concept] text box. Select the term that best matches your input.
    physiology_DE_ranking

7. Click [Continue] after the entering the input.  This will bring you back to the [Rank Selection] tab.

8. Click [Get Ranking] to view the result table. The [Differential expression] column shows the maximum log2FoldChange for a given disease, compound, or phenotype. 

Note: The [Classification] column contains short description for each gene in the table.

ranking_results_disorders_DE9. In the result table:

  • Click on the [Differential expression] column header to sort the genes based on log2FoldChange values
  • Click 0n the log2FoldChange value to get details on the differential experiment in which the value is extracted.

10. Click [All] in right-hand corner of the table to save the results in a csv file.

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