ProteinCenter User Manual
Table of Contents

Chapter 14. Proteins view

Table of Contents

14.1. The proteins view

14.1. The proteins view

The proteins view displays a list of proteins with possible experimental data summaries for each protein. Each line corresponds to a unique protein (i.e. unique amino acid sequence in a given species, cf. Chapter 4, The Protein record )

The result of a lookup or choice of a dataset from the workspace or the basket is by default shown in the proteins view.

Besides displaying protein descriptions and protein keys, annotation is provided to put the list of proteins into its biological context. This includes a variety of predictions of the molecular structure, biological function and cellular targeting of the protein. Furthermore, it includes information regarding outdating of proteins and imported user data as described below. The view is intended to provide an instant overview of what is known about the proteins.

Figure 14.1. The protein view (truncated to the right)

The protein view (truncated to the right)

Below is a short description of the most common columns in the proteins view. To manually select which columns to display, see Section 5.4.5, “Selecting which columns to display”.

  1. The proteins view is found on the Proteins pane

  2. The filter component for filtering the list of proteins - more information in Chapter 11, Filters

  3. Paging functionality as described in Section 5.4.3, “Paging functionality”

  4. Acc.Key - The protein key is the protein identifier (GI, Ensembl, UniProt, FlyBase, PlasmoDB, SGD, TAIR, IPI, etc.) of preferred choice. See also canonical identifiers Section 4.3, “Preferred accession” & explanation of protein keys Chapter 26, Vocabulary

  5. No - The number of experimental data for the protein. Click on the number to see the details

  6. Protein outdated status - The protein status field flags outdated protein records. If the symbol is present, then the protein record has become outdated. See Section 4.2, “Versioning and outdated entries” for more details

  7. Description - The general descriptive information stored with the particular protein key

  8. Select protein - A checkbox for selection of protein entries

  9. Button for saving all selected protein to a new dataset/folder

  10. Button for deleting the selected proteins from the dataset

  11. Select all proteins in the dataset

  12. Deselect all selected proteins in the set

  13. Add protein to Basket - Click the basket icon to add this protein to the basket. For more details on the basket please refer to Chapter 8, The Protein Basket

  14. Cluster Identifier - The identifier for the cluster (if data is clustered). For more details please refer to Chapter 16, Clusters View

  15. Gene - The official symbol that has been used for this gene and its products

  16. AA - The number of amino acid residues in the protein sequence

  17. AS - Flagging (with ) of proteins known to be products of alternatively spliced genes. If tagged with a "1" ( ) - the given protein is one particular splicing isoform

  18. Fr - Flagging of N- or C- terminal (non-biologically) truncated proteins arising from incomplete data base entries.

  19. Tax - Species are abbreviated to two letters for organisms commonly used in molecular biology projects and to three letters for remaining species. See Table C.1, “Abbreviations for commonly used organisms” for the list of abbreviations. By pointing the mouse to the field, the full species name is displayed.

  20. Molecular Function - GOslim Molecular function colour summary created from consolidation of GO data - Please refer to GOslim Appendix Table D.2, “GOslim categories for Molecular Function” for details.

  21. Cellular Components - GOslim Cellular component colour summary created from consolidation of GO data - Please refer to GOslim Appendix Table D.1, “GOslim categories for Cellular Component” for details.

  22. Biological Processes - GOslim Biological process colour summary created from consolidation of GO data - Please refer to GOslim Appendix Table D.3, “GOslim categories for Biological Process” for details.

  23. TM - Number of transmembrane domains predicted by TMAP.

  24. Signal - Prediction by PrediSi with a threshold > 50%. The icon flags the presence of a signal peptide.

  25. The number of experimental peptides for the protein. Clicking on the number will open the ProteinCard for that protein with the peptide details ( Section 10.2.2, “Peptides details” ) shown

  26. All supplementary data are shown with configurable statistics columns. For more details on individual columns see Chapter 13, Protein data view

Furthermore, there are two optional columns not shown by default, which can be activated by the column selector:

  • Mono. mass - The monoisotopic mass of the protein sequence

  • Avg. mass - The average mass of the protein sequence

It is possible to view the detailed experimental data for any given protein within the protein view, as shown in the figure below, where the 'No' column for protein 62750354 (at '4') was clicked to expand the box shown below with four experimental data points.

Figure 14.2. Expanding protein data inside the protein view

Expanding protein data inside the protein view

The protein data can be hidden by clicking at '4' again.

Related views: