Expression Data Import Service

Overview

The Differential Expression Import Service allows you to upload your own pre-processed differential expression datasets generated by microarray, RNA-Seq, or proteomic technologies to your private workspace and analyze them using annotations and analysis tools and compare them with other expression data sets in PATRIC. Currently, PATRIC only supports differential gene expression data in the form of log ratios, generated by comparing samples/conditions/time points.

The Differential Expression Import Service can be accessed from the Services Menu at the top of the PATRIC website page and via the PATRIC Command Line Interface (CLI).

Experiment Information

Specify Experiment Title/Description, Organism, and Pubmed ID for keeping track of uploaded data.

Data information

What is this?

At PATRIC, you can upload your own pre-processed differential expression datasets generated by microarray, RNA-Seq, or proteomic technologies to your workspace and analyze them using annotations and analysis tools. Currently, PATRIC only supports differential gene expression data in the form of log ratios, generated by comparing samples/conditions/time points. You may also compare your data with other transcriptomics datasets available at PATRIC. Data uploaded in your workspace is private and protected.

Experiment Data

Upload a data file containing differential gene expression values in the form of log ratios. The file should be in one of the supported formats described below. Optionally, you may also upload metadata related to sample comparisons in the prescribed format to help later in the data analysis.

Supported IDs

  1. RefSeq Locus Tag
  2. PATRIC Feature ID
  3. NCBI GI Number
  4. NCBI Protein ID
  5. SEED ID
  6. PATRIC Legacy ID

File Format

Currently, PATRIC allows you to upload your transcriptomics datasets in the form of differential gene expression measured as log ratios. Data can be uploaded in multiple file formats: comma separated values (.csv), tab delimited values (.txt), or Excel (.xls or .xlsx). Click to download Sample Data template in Gene Matrix Format. Files should contain data in one of the following formats:

  1. Gene Matrix:

    Gene ID Comparison1 Comparison2
    b0002 0.767 -1.316
    b0003 0.815 -1.841
    b0004 0.856 -1.643
  2. Gene List:

    Data is presented in three columns: Gene ID, Sample ID, and expression value. Expression value should be in the form of log ratio (i.e. log2 (test/control)).  Below is an example of transcriptomics data in Gene List format:

    Gene ID Comparison ID Log Ratio
    b0002 Comparison1 0.767
    b0003 Comparison1 0.815
    b0002 Comparison2 -1.316

Experiment Type

This field specifies the the experiment type Transcriptomics, Proteomics, or Phenomics.

ID Type

In order to take full advantage of PATRIC data, gene ID’s provided in the experiment data are mapped to PATRIC. Due to differences in annotation that may exist some genes may go unmapped. Unmapped genes will be excluded from subsequent analysis.

File Type

This field specifies whether the uploaded Experiment Data File is tab/comma delimited or an excel file.

Optional Metadata

PATRIC allows you to upload an additional file containing key metadata attributes about the comparisons. This will enhance your analysis when using the Heatmap and clustering tools. The metadata table can be uploaded as a tab/comma delimited or Excel file. Note: The column names should be the same as in the example template. Also, comparison IDs in the metadata file should match those in the data file. Click to download Metadata Template