Gene Page Transcriptomics Data

Gene Page Transcriptomics Data Overview

The Transcriptomics Tab at the gene-level summarizes the expression of a gene in all available experimental datasets. All the comparisons in which a gene is differentially expressed are listed in a table along with associated metadata such as Strain, Gene Modification, and Experimental Condition. Expression value based filters and a graphical summary of the experimental metadata allow you to quickly find top experimental conditions and gene manipulations related to the differential expression of the gene. This may help to confirm or infer potential function of the gene.

Accessing Gene-Level Transcriptomics Data

Gene-level transcriptomics data is available under the Transcriptomics Tab on any given Gene Overview Landing page. You may search for your gene/CDS of interest using PATRIC’s Global Search and then go directly to the corresponding Gene Overview Landing page.

Using Transcriptomics Data at the Gene Level

  • The data may be filtered, via the controls above the graphs, in the following ways:
    • Use the keyword search box to find the comparisons with matching descriptions or metadata. Some examples of keywords: "mutant", "rpoS", "temperature", and "oxygen".
    • Apply the |Log Ratio| and/or |Z-score| cut-off to see only those comparisons in which the gene expression passes the cut-off. This, in addition to the graphical summary of the metadata, allows for quickly locating experimental conditions that cause significant differential expression of the gene.
    • Reset the filters back to the default mode or click on Show All Comparisons to see all the comparisons in which the gene is reported.
  • The Log Ratio and Z-score distribution graphs provide a quick visual summary of the number of comparisons in which the gene is significantly expressed.
  • The pie/bar graph of key metadata attributes, such as Strain, Gene Modification, and Experimental Condition allows for quickly locating top gene modifications or experimental conditions causing differential expression of the gene.
  • The table below the graphs lists all comparisons matching the current filtering criteria. It provides link-outs to corresponding NCBI publications (PubMed) and GEO experiment pages (Accession). The table may be sorted based on any of the columns or downloaded as a text/Excel file.

Correlated Genes?

For a gene of interest, the Correlated Genes tab shows a list of genes that have correlated expression profiles (positively or negatively) across all available data sets along with their functions. Thus, researchers may identify genes that are co-regulated or have similar functions. It can also help to infer potential function of a hypothetical or unknown gene.

Working with Lists of Correlated Genes

  • Filter the list by specifying any correlation cut-off (between 0 and 1) and positive/negative correlation.
  • Use the Gene List Table Toolbar located in the light blue row to:
    • Save selected items to groups within your Workspace by clicking the Add Feature(s) button. To learn more about how to save data for future visits and utilize your personal Workspace see Workspace FAQs.
    • View or download selected DNA and/or protein sequence data in FASTA format. The individual tables themselves, or selected data within them, are also downloadable in both excel and txt file formats.
    • View pathways and associated pathway information for your selected genes by clicking the Pathway Summary button.
    • Conduct Multiple Sequence Alignment analysis on selected groups, or selected items within groups, by clicking the Multiple Sequence Alignment button. For more details on this tool please see Multiple Sequence Alignment FAQs.
    • Utilize the ID Mapping Tool on selected items by clicking the Map IDs button. For more information on this tool please see ID Mapping FAQs.
    • Customize columns shown/hidden in your results table with the Columns button.