Report Pages

All objects in BovineMine (e.g., gene, protein, transcript, publication) have report pages that can viewed after running a query. It allows users to view all available information for that object while providing links to related objects. As an example, we can revisit the template Gene ⮕ Homologues. In the list of templates under the Templates tab on the BovineMine home page, select Gene ⮕ Homologues to query BovineMine to retrieve all homologues for a given gene. Enter RCAN1 into the LOOKUP search box (by default it should already be entered) then click Show Results. In the results table, note that every entry is contains a link. You can mouse over any link to bring up a summary of that object. If we hover over the first Gene ID, we can see a summary box that includes the gene’s biotype, chromosome assembly, description, length, organism, symbol, and source.

Report summary box — Summary for gene entry in query results table

Clicking on that same item will bring up its report page that includes a comprehensive for gene RCAN1. The report page header shows the Gene ID and its Biotype, for this example, protein coding. The tabs at the top of the page in the Quick Links menu bar quickly bring you to the data listed. The column on the right side of the report page displays external links to other Mines and databases.

The content of the report page is divided into categories based on the type of information provided for that particular object. Clicking on links within each category bring up more details about the objects of interest.

Summary

The Summary section near the top of the report provides information on the gene such as its length, chromosome location, and strand information. Users can also get the complete FASTA sequence of the gene by clicking on the FASTA tab.

Alias and DBxref

The Alias and DBxref section displays tables of aliases and database cross references for the gene. In this example, the RefSeq gene ID has one cross reference to an Ensembl gene ID.

Transcripts

The Transcripts section contains information about the gene model, such as transcripts and exons. It includes a diagram visually representing each transcript with its features highlighted (if applicable). Links to FASTA files are included where applicable. In the case of protein coding genes, a table with protein information is also provided.

Proteins

The Proteins section provides information about the protein product of the gene. The comments section gives a brief description about the protein along with the UniProt accession and links to any outside data sets.

Function

The Function section displays Gene Ontology annotations for a gene. Annotations are divided into three categories:

Cellular Component
Molecular Function
Biological Process

The GO terms are displayed along with the evidence code indicating how the annotations were derived. A results with Pathway information is also displayed if applicable.

Homology

The Homology section provides information for all homologues. The first portion displays a summarized view of the homologues reported in different organisms. The next portion provides more detailed information about the homologue, the type of homologue and from which dataset the information was obtained all displayed in a results table.

Publications

The Publications section displays a table of publications related to the gene with links to full citations.

Other

This last section provides miscellaneous information that do not fit into any of the above categories. This example lists data sets and synonyms.