micro RNA
miRNA (also written microRNA or µRNA) are non coding RNA that are not translated into proteins. Instead they normally control the translation of mRNA. Profiling miRNA levels, using microarrays is becoming a widely used technique. Key functionalityWith Qlucore Omics Explorer the researcher can easily examine and analyze data from miRNA experiments. For miRNA profiling the following functionality will be of specific interest: - Check data for outliers by visual inspection using sample Principal Component Analysis (PCA) plots.
- Perform statistical analysis using ANOVA.
- Remove unwanted factors (batches) with a single mouse click.
- Use hierarchical clustering or PCA to indentify subgroups.
- Generate a list of miRNA 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 miRNA.
| 
|
Platform specific data import
Qlucore Omics Explorer supports data import from several sources, both from Next Generation Sequencing (NGS) and arrays. If you are using arrays from the companies listed below, a brief description of the required import steps is also provided. If you have NGS data please see the Support section and the FAQs. Note 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.
Agilent: Qlucore Omics Explorer can import and normalize data generated with the Agilent Feature Extraction software. Export data using the single file option. See the features section (menu at top right) and the document How to import data for more details.
Affymetrix: Affymetrix provides the software tool Mi RNA QC for free; see www.affymetrix.com. Start the MiRNA QC tool. Load your .cel files and then start the analysis by selecting "Run analysis". When the results are presented, go to the menu item "Tables and Intensities". Display the main table and save the table as a tab separated text file. Start Qlucore OE and import the file using the Open command in the File menu.
Exiqon: Exiqon offers on their website descriptions and a workflow on how to extract data from their arrays using the Agilent Feature Extractions software(see http://www.exiqon.com/microrna-array-analysis-using-feature-extraction). Follow the instructions on then Exiqon website and then continue using the instructions for Agilent above.
Illumina: Illumina provides the Genome Studio Software where the GX module handles miRNA 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 Ncode Profiler Software for free; see www.invitrogen.com. It is possible to export normalized data as a tab delimited text file. Start Qlucore OE and import the file using the Open command in 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.