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Foundational Concepts

This section provides a quick introduction to some key concepts that underpin the entire Geneweaver ecosystem. This section should be enough to get you started, but for a comprehensive definition, please see the Concepts section.

Genes (Genomic Features)

In GeneWeaver, a "Gene" 🧬 is a unique identifier for a gene in a particular organism. Genes are the basic unit of analysis, and are used to build GeneSets. GeneWeaver identifies genes using their unique identifiers, which are called "Gene Identifiers". A gene identifier is a unique name or number assigned to a gene.

GeneWeaver supports a variety of different Gene Identifiers from different sources, including Ensemble (Gene, Protein, and Transcript), MGI, HGNC, and Entrez. Internally, each Gene Identifier is mapped to a unique Gene ID, which is used to identify genes across all data sources.

For more information about Genes and GeneSets, please see the Genes and GeneSets page.

GeneSets

The central entity in GeneWeaver is called a "GeneSet" 🧬+📂. A GeneSet is a collection of genomic features that are related by a common biological function, pathway, process, or other biological concept. GeneSets are used to organize and analyze heterogeneous functional genomics data.

Genesets are a fundamental component of Geneweaver, as the system uses them to perform integrative analysis of functional genomics data. Researchers can compare and combine multiple genesets to identify overlaps or similarities, which can provide insights into the biological processes and pathways that are involved in the data being analyzed.

Species

Genomic features in Geneweaver are mapped within and across multiple species. Cross species analysis enables the discovery of conserved mechanisms of biological functions, and the discovery of divergent functions served by conserved biological mechanisms.

Currently, 10 species are supported:

  • Mus musculus - The Mouse 🐁
  • Homo sapiens - The Human 🧍
  • Rattus norvegicus - The Rat 🐀
  • Danio rerio - The Zebrafish 🐟
  • Drosophilia melanogaster - The Fruit Fly 🪰
  • Macaca mulatta - Rhesus Monkey 🐒
  • Caenorhabditis elegans - The Roundworm 🪱
  • Saccharomyces cervisiae - Brewer's Yeast 🍺
  • Gallus gallus - The Chicken 🐓
  • Canis familiaris - The Dog 🐕