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GeneSet Utilities

GeneSet Details Pages allow users to view vital information about gene sets of interest, including associated genes, homologs and references to external links. Gene Intersection Lists are useful for determining which information is shared between gene sets of interest. In addition, GeneWeaver tools allow users to Combine gene sets of interest or perform more complex set operations based on Boolean Algebra. Gene sets may also be annotated with information about * Emphasis Genes*, allowing users to augment GeneWeaver tools with gene-specific information.

Emphasis Genes

The Emphasis Genes utility enables users to select genes or an entire set of genes that may be highlighted in various analysis tools.

To set emphasis genes choose "Emphasize Genes" from the Analyze GeneSets drop-down on the navigation bar or from the footer.

The current emphaisis genes are listed on the left side of the page.

To modify your emphasis genes, you can remove genes one at a time using the "x" icon next to each gene. To clear the entire list, click the "Clear all genes" button at the top of the page.

To add a gene, type the gene name or part of it in the box on the right side of the page. A list will appear based on the partial name. Select one and click the "Go" button.

The gene or genes if the selection included several, will be listed on the page. Use the "Add all genes" or "Add" link to select the desired gene(s).

Homology Mapping

GeneWeaver uses the concept of Homology Mapping to expand search and analysis capabilities beyond a single species. Currently, we rely on data provided by Homologene to assert homology between clustered sets of reference gene ids. That is, GeneWeaver creates a set of unique id clusters (representing Entrez, Ensembl, Gene Cards, etc.) representing specific genes, these clusters are connected across species using mappings established by Homologene.

Gene Intersection Lists

Gene Intersection Lists are useful for determining which information is shared between gene sets of interest.

Gene intersection lists can be generated by clicking on the output of various tools including the Hypergeometric tests, Jaccard similarity matrix Venn diagrams and HiSim Graph nodes. A table of genes by GeneSets is displayed. Next to each gene symbol are links to gene specific queries of external resources. Each gene has links to associated databases, such as NCBI, Ensembl, STRING, MGI, GeneNetwork, etc. For users with the FireGoose GAGGLE extension installed, you will also find the genes on the page available for broadcast on the page. Filled circles indicate the presence of a gene in a GeneSet. Green (light) circles indicate that the exact gene is present in multiple gene sets. Dark (maroon) circles indicate a homologous gene is present in multiple gene sets. The table can be exported using the export .csv feature at the bottom of the window.

Combine

GeneWeaver tools allow users to combine gene sets of interest. GeneWeaver tools operate on a weighted bi-partite adjacency matrix, a table of Association Scores in a Gene (row) x GeneSet (col) tab delimited text format. For many GeneSets, the scores are binary.

To create sample GeneWeaver data for development or off-line analysis:

  1. Perform a database query using the search field.
  2. Add the GeneSets to a project.
  3. Go to the "Analyze GeneSets" page.
  4. Select the project or specific GeneSets from projects.
  5. Select the "Combine GeneSets" tool, pick homology included or excluded and click run.
  6. Save the file to your computer.

External Data Resources

GeneWeaver contains publically available sets of genes annotated to structured vocabularies and ontologies that are assigned Tier I, or public resource data. Other sets of genes, such as MeSH term-to-gene annotations, are derived from the processing of public sources and attributed to Tier II. In the case of MeSH, we take advantage of NCBI’s gene-to-Pubmed and Pubmed-to-mesh files to produce sets of genes annotated through their transitive associations.