Tutorial: Deep Dive into Gene Selection and Insights
In this tutorial, you will learn how to explore, search, filter, inspect, and export genes in the Gene Selection view, and how to use built-in tools to gain detailed context and actionable insights from the literature.
Step 1: Explore the Gene Selection View
Follow the steps below. Use ←/→ to navigate; press 1-9 to jump.
Step 1 of 8
After annotating your articles with PubTator3, all recognized genes appear in the Gene Selection view.
The main table lists every annotated gene, while the right-hand panel displays the genes you have actively selected for downstream enrichment.
Your selection can be updated at any time. Genes added to the right panel form the input set for enrichment analysis.
Use the search bar to locate genes by their symbol, or enable Deep Search to also include how genes are mentioned in the text.
For example, the mouse gene App (Entrez ID: 11820) may appear as APP, Abeta, or amyloid precursor protein. Deep search ensures all variations are found.
Deep search is essential when genes have multiple aliases or are frequently referred to by descriptive names.
The Species Filter menu lets you narrow the table to genes from specific organisms.
Select one or more species to filter. If none are selected, genes from all taxa are shown.
Ideal when working with literature involving multiple species, such as human and mouse data.
You can search by gene symbol, Entrez ID, Taxonomy ID, or by selection status directly in the table (1 & 2).
Clicking a column header sorts the table by that column; click again to reverse the order (3).
Sorting by annotation frequency or GF-IDF score is useful for prioritizing genes based on relevance.
A right-click on any gene in the table opens a context menu with powerful selection and information tools:
Select top genes: Opens a small dialog to choose how many top-ranked rows should be selected. All current selections are cleared first, and the top n rows are selected automatically.
Select by tax ID: Opens a multi-selection dialog for species. After choosing taxa, all genes belonging to those species are automatically selected.
Open gene info: Opens the NCBI Gene page for the selected gene directly inside pathXcite's embedded Web Browser in a new tab.
These options speed up selection workflows and make it easy to retrieve external reference information without leaving the tool.
Click the Export icon to save your gene list. Choose whether to export all genes or only those you selected.
You can also choose to export only gene symbols or include full metadata (symbol, Entrez ID, count, tax ID, GF-IDF score).
Export options: CSV, TSV, JSON, and TXT. Use "Select export path" to set the save location.
Clicking a gene in the right-hand panel opens a detailed view of its mentions across the literature (1).
You'll see how it was written in the text, the PubMed ID, the section where it appears, and the text offset location.
Use “Copy symbol” (2) or “Copy Entrez” (3) for quick clipboard access, and “Show sections” (4) to reveal where in the paper the gene is mentioned.
The detail panel also provides helpful statistics (1):
Number of documents containing the gene
Number of unique sections it appears in
Total mentions across the entire article set
These insights give you a deeper understanding of the gene's context, usage, and relevance to your topic.
Resize the detail panel to view it in a wider format (2).
Great job! You now know how to search, filter, inspect, and export genes, use the context menu for efficient selection, and explore gene mentions in detail.
You're ready to use your curated gene list in enrichment analysis.
