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Protein Array

Protein arrays provide a powerful way of detecting proteins and monitoring their expression levels. Protein arrays have become one of the most active areas emerging in biotechnology. The objective behind protein array development is to achieve efficient and sensitive high throughput protein analysis.

 

Key functionality

With Qlucore Omics Explorer, the researcher can examine and analyze data from protein array experiments. The following functionality will be of specific interest:

  • Investigate any structures in the data by using variance filtering combined with Principal Component Analysis (PCA) and hierarchical clustering.
  • Perform statistical tests using ANOVA to enhance results.
  • Generate a list of proteins that classifies data based on a selection of statistical tests: F-test, t-tests or regression.
  • Work with Variable PCA plots to find correlation and networks among selected proteins.

 

Screendump

Platform specific data import

Qlucore Omics Explorer supports data import from a number of different sources. If you have used an array from the companies listed below, a brief description of the required import steps is also provided. Please note, however, that Qlucore Omics Explore expects data to be normalized before input. If you have data from other sources, please see the general data import section.

Illumina: Illumina provides the Genome Studio Software. The PT module handles protein data. Data can be exported in various formats which are easily imported into Qlucore Omics Explorer. See the Illumina product documentation on how to export a normalized ".txt" file. Start Qlucore OE and import the file using the Open command from the File menu.

Invitrogen: Invitrogen provides the Protoarray Prospector software for free (see www.invitrogen.com for more details). The Protoarray Prospector software automatically generates a file called "Comparisons Results.txt" in the same folder as the Prospector software resides. That file is generated when two or more arrays are compared. Start Qlucore OE and import the file using the Open command from the File menu.

 

General data import

Use generic formats: If your file match the simple or compact text file formats supported, data can be imported directly, see the features section (menu at top right) and the document How to import data for more details.

Convert manually: Most data generated from protein array experiments can easily be converted to the Qlucore platform independent data format ".gedata" or to the compact text or the simple text format supported by Qlucore Omics Explorer. The ".gedata" format allows both data and annotations in the same file, the simple text format supports data. The annotations can be imported separately. Conversion is at best done in a spread sheet program as Excel. More information about the ".gedata" and the simple and compact text formats can be found in the features section (menu at top right) and the document How to import data.

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