Findings from ProteinCenter can be documented as PDF reports. Reports differ from exported files in that they are formatted to be read by humans rather than programs. This means that the export functionality described in Chapter 23, Export may be more convenient, if reporting datasets for further analysis in other tools or programs.
After selection of a dataset (and possibly application of filters, clustering and comparisons) go to the report pane in the navigation menu:
A status message will display the number of proteins that will be included in the report. This number depends on the dataset, the filters applied, the proteins selected and the row selection made in item 6.
Choose report type. Several different report types are available:
Proteins - a summary view for each protein, reminiscent of the Proteins View (see Section 24.2, “The Proteins report”).
GO Slim - a summary view of the GO Slim basic types: Cellular Component, Biological Process and/or Molecular Function (see Section 24.3, “The GO Slim reports”).
General Info - a page of the most basic information describing the data, akin to the μLIMS view. (see figure Figure 24.1, “The General Info page”).
Currently, the only available report format is PDF.
The file name of the report is the name of the dataset or comparison followed by _report.pdf.
Specification of the rows to be included in the report. Two sets of radio buttons can be set:
Selected/All - only include proteins that has been selected (e.g. after filtering) or include all (i.e. disregard selections).
Anchors/All - include only anchor proteins or include all proteins from the dataset.
Checking the Include info page checkbox will attach a general information page as the first page of the report. (see figure Figure 24.1, “The General Info page”).
Click the Report button to create the actual report.
You can choose to save the report to disk, or open it directly.
This is a report of a chosen set of proteins, similar to the Proteins View. An example of its use could be as documentation for protein identifications.
For a comparison study, columns are included to show dataset affiliation, and the datasets will be specified in a legend at the bottom of the report.
Supplementary data for the dataset will be fitted at the end of each protein line, as much as space allows. In the general case, each supplementary data type can have multiple values for a protein, and these are represented by the median for numeric types, and the mode (i.e. most frequent term) for string types. Links are not shown for proteins. If certain supplementary values can not fit in a column in the final PDF report document, the full value can be revealed by hovering over the truncated value with the mouse.
Clicking the name or dataset path in the final PDF report document will take the viewer to the dataset in ProteinCenter.
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