This section shows how to access and filter the results of the analysis.

NOTE

Periodically, the FASTA files provided by the Annotation Server or UniProt are updated. The minor changes in an updated file cause minor changes in the results. The changes are not important in this context. Your results will be nearly identical.

Procedure

  1. Access the results by using one of the following methods:
  2. Select the Analysis Results tab in the study and do one of the following:
    - Double-click the row with the result ID 1.
    - Highlight the row, and select Open Result to open the result file in a separate tab.
  3. Open the Job Queue by selecting Administration > Show Job Queue, and do one of the following:
    - Double-click the row in the Job Queue for the Consensus workflow that just finished.
    - Highlight the row, and select Open Result to open the results in a separate tab.
  4. In Windows Explorer, find the study folder, and open the result file.
  6. Select the Report Item Distribution Charts icon, and then select the PCA plot tab.
  8. In the Color By section the upper left of the PCA plot, clear Yeast Strain and the select the File checkbox.
  9. The PCA plot shows a separation between the results of the two data files. The separation is due to the use of the Abundances columns from the Proteins table rather than scaled abundances. The following image shows the display from scaled abundances.
  11. From the Data Source dropdown list, select Proteins: Abundances (Scaled).
  12. For Color By, clear File and select Yeast Strain.
  14. The following image shows that the replicates of each yeast strain now cluster between both files in the PCA plot based on the scaled abundances.
  16. Select the Volcano Plots tab in the Report Item Distribution plots.
  17. In the Comparison dropdown list, select Met6 vs. Parental.
  19. Double-click the point in the upper left corner, which corresponds to the MET6 protein that is knocked out in the Met6 strain.
  21. Select the Quan Channel Values plot icon.
  23. Right-click the Quan Channel Values panel, and select Show Ungrouped Abundances.
  24. The plot updates. Though there are two data files, the channels for the different data files rescale to show consistent abundances across all the quan channels.
  26. Select the Heat Map tab in the Report Item Distributions window.
  27. (Optional) Resize the Report Item Distributions window by hovering the pointer on the right side of the window, selecting, and dragging the window to the right.
  28. Select Refresh in the Heat Map window.
  30. The following image shows that the channels cluster first by file and secondly by yeast strain.
  32. For Data Source, select Proteins: Abundances (Scaled), and select Refresh.
  33. The following image shows the new plot with the vertical axis clusters primarily by yeast strain instead of by file.
  35. To see which pathways are highly up-regulated in the Met6 knockout, move the pointer to the region shown in the following image to highlight the cluster of proteins, and double-click to zoom.
  37. Right-click the plot, and select Check All Visible Points.
  38. Select the Enrichment Chart icon.
  40. In the Enrichment table, select Reactome Pathways as the Annotation Source, and select All Identifiable Proteins as the Background.
  41. The following image shows that the Citric Acid Cycle is the most enriched pathway, with 6 of the 17 proteins expressed in the selected cluster.