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Database Search Guide ​

The Database Search feature in Omics Studio allows you to query external knowledgebases for detailed information about genes and proteins. It integrates resources such as UniProt, Reactome, and the Human Protein Atlas (HPA), giving you quick access to functional, structural, and expression data. This guide explains how to navigate the Database Search interface, perform queries, and interpret the results.

  1. In Explorer, select the Database Search icon (magnifying glass) from the left-hand navigation. The Database Search page opens.
  2. At the top of the page are tabs for different knowledgebases: UniProt Knowledgebase, Reactome, and Human Protein Atlas (HPA) – Protein. Each database has its own result table and sub-categories (such as Molecular Identity, Structure & Features, Function & Interaction, etc.), which correspond to the types of information you can retrieve.

Searching the UniProt Knowledgebase ​

The UniProt Knowledgebase tab is selected by default. It provides curated information about proteins.

  • Search bar and pagination: Use the search field to filter entries by UniProt ID, gene symbol, or keyword. Navigate pages with the Go to page box or pagination buttons.
  • Results table: Default columns include UniProt ID, Gene Names Primary, and Reviewed/Unreviewed status. Each row represents a protein record.
  • Selecting a record: Click a row to view detailed annotations in the Details panel. For example, selecting TP53 (UniProt ID P04637) shows sections such as Activity Regulation, Interacts With, Tissue Specificity, Involvement in Disease, and Mutagenesis. Additional metadata includes IDs, gene names, organism, annotation evidence, and PubMed references. Use Show more to expand truncated text.
  • Data categories: Switch between Molecular Identity, Structure & Features, Function & Interaction, and Expression to explore domains, post-translational modifications, interactions, or expression data.

Searching Reactome ​

The Reactome tab provides pathway annotations linking proteins to curated biological pathways.

  • Results table: Columns include UniProt ID, Reactome Protein Identifier (R-HSA), and Source ID. Use the search bar to filter results.
  • Viewing details: Selecting a row opens the Details panel with identifiers, pathway name, curation confidence (e.g., TAS, IDA), organism, oncology classification, and pathway level. Hyperlinks connect directly to Reactome pathway pages.
  • Sub-categories: Switch between Molecular Identity, Function & Interaction, and Expression & Localization for different annotation types.

Searching the Human Protein Atlas (HPA) ​

The Human Protein Atlas (HPA) tab focuses on protein expression and localization data.

  • Results table: Default columns are Ensembl ID and Gene Name. Use the search bar to filter records.
  • Viewing details: The Details panel shows tissue-specific expression data: tissue/cell type, IHC tissue name, expression level (not detected, low, medium, high), and reliability (approved or uncertain).
  • Sub-categories: Includes Expression & Localization and Experimental Evidence & Curation, which provide subcellular localization and evidence-level details.

Tips for Effective Searching ​

  • Use the search bar: Narrow results by gene symbol or identifier (e.g., TP53).
  • Navigate pages: Use pagination controls or Rows per page to adjust table display.
  • Review metadata: The Details panel contains curated comments, cross-references, and links to external databases.
  • Switch categories: Use sub-tabs to filter by structural, functional, or expression-related annotations.

Summary ​

The Database Search tool in Omics Studio aggregates curated protein and gene information from external resources. You can:

  1. Choose a knowledgebase (UniProt, Reactome, or HPA) and optionally a sub-category.
  2. Use the search bar to filter records by gene name or identifier.
  3. Navigate through large result sets using pagination controls.
  4. Select a row to display detailed annotations in the Details pane, including functions, interactions, pathways, expression patterns, and references.

This integrated search capability allows you to enrich your omics studies with up-to-date biological context and supports the creation of custom gene lists for downstream analyses.