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Overviewing patterns of a selected gene over all series.

Overviewing a lot of multi-omics data sets in your Subio Platform.

When dealing with a vast number of Series spanning multiple Platforms and Organisms, opening and inspecting each one individually becomes an overwhelming task. The Scan Genes Over Series tool solves this by providing a bird's-eye perspective.

In essence, it allows you to perform searches on your local Subio Platform data similar to the NCBI GEO Profiles tool. The key advantage is that you can search for and compare two genes simultaneously. This tool helps you quickly answer questions such as:

  • In which Series is the expression of these genes exceptionally high?
  • Which Series show significant fluctuations in these genes?
  • •In which Series do these two genes exhibit highly similar expression patterns?

Important Tips for Effective Use

  • Vertical Axis & Data Type:
    The graph's vertical axis represents the Ch1 Raw Signal. To ensure consistent and meaningful results, ensure that you import and store values as close to the raw data as possible (e.g., MAS5 rather than RMA for GeneChip or Gene Counts rather than FPKM/TPM for RNA-Seq).
  • Search by Gene Symbol:
    The tool searches using Gene Symbols. Since Feature IDs are often Probe IDs or ENSEMBL IDs, ensure you use the Select Symbol Column button in the Platform list toolbar to designate the correct column.
  • DataSet Organization:
    The tool displays the topmost DataSet in the list. For the best results across all Series, we recommend placing an "All Samples" DataSet at the top of the DataSets section. This DataSet should:
  1. Display individual samples (no averaging/grouping).
  2. Show all parameters necessary to get a complete overview of the Series.
  • Database Preparation:
    Generating the search database is a heavy process. It won't be ready for immediate use the first time you initiate it. We suggest starting the database construction before leaving for the day or during a break so it is ready when you need it.

If you have any questions regarding the operation of this tool, please feel free to apply for our free online support.