Gene metadata table

Modified on Fri, 03 Nov 2023 at 09:36 AM


With gene metadata table you can explore additional information on your genes of interest via an interactive table. This information can be acquired from a variety of databases, access to which is determined by your subscription. 

1. Creating a plot 

To create a gene metadata table frst click on the create plot icon in your analysis track. This will open the Create plot page.

In the Create plot field you can set a name and description of the plot. Subsequently under Choose algorithm to run your analysis select "Gene metadata table". Once you have selected this option, a new field called "Select database" will appear. 

2. Selecting a gene metadata database as input

In the field Select database, you can pick from which databases you would like to perform pull gene metadata. The database version is displayed in brackets. Once you have selected a database from the dropdown menu confirm you selection by clicking on the Select database button.

3. Setting parameters

In the Set parameters field you can specify for which genes of interest you want to acquire which gene metadata attributes. The gene groups you specify in the Selected feature tab will be available in the gene metadata table. The available choices here are:

  • All
  • Metabolic
  • Transcription factors
  • Transporters
  • Cell surface
  • Custom

Selecting the "All" option will limit which attributes you will be able to select in the "Attributes of interest". The attributes that will not be displayed are: 

1. Interactions
2. GeneHancer database
3. Variants
4. Unified compaunds
5. Unified drugs
6. Publications

If you select the Custom option a new multi-select menu will appear where you can enter the gene symbols of your genes of interest.

In the Attribute of interest tab, all of the attributes of the gene metadata database are displayed in a dropdown menu. From here you can select on attribute of interest which will be available in the gene metadata table. 

4. Creating the gene metadata table

When you have these settings set you can click the Run button to create the gene metadata table. I will appear as a new plot in your track from which you can select it and view it as an interactive plot.


5. Gene metadata table interactive plot page

In the interactive plot page you can explore the results of the gene metadata table via a pivot table.

6. Gene metadata table as a input for the rule-based meta-analysis

This newly created can be selected as input in the rule-based meta-analysis. When setting up the rule-based you can set the rules for the gene metadata table via a gene selection pivot table. You can use it to make a selection of your genes of interest based on if they satisfy gene metadata criteria. You can make selection for both categorical and numerical variables. The resulting gene selection table will display all your genes of interest and wheter they pass your selection criteria. 

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