Xenbase Release Notes

Release 2.8

• Added antibody pages and search interface
• Added protein tab to gene pages
• Summary images on gene page summary auto-rotate

Release 2.7

• Added NCBI Entrez Gene ID as a searchable field for gene pages.
• Links to the Ensembl and UCSC genome browsers added for each gene page, where applicable.
• Gene page and clone page expression tab restructured. Expression images can now be sorted by various criteria, such as stage.
• Added the ability to exclude anatomy terms from a gene expression search.
• Added the ability to search clones by anatomy item.
• Added search all option to the literature search, along with the ability to filter queries by date range.
• Expression tab added to anatomy item pages, listing genes expressed in the tissue, along with expression sources.
• Reagents and protocols menu added to the main Xenbase menu bar

Release 2.6.5

• Implemented Textresso for Xenopus. Textpresso is a powerful text-mining system for scientific literature.
  • Search paper titles, abstracts, results, discussion,etc using keywords or phrases.
  • Selecting one or more Categories, which are pre-defined word-lists, increases the specificity of a search. Categories include Xenopus gene symbols and synonyms, the XAO, and GO terms.
• Pages created for XAO anatomy items and development stages.
• Includes a tab for displaying papers attributed to the XAO term via text matching.
• Includes a wiki tab for users to submit content.
• Xenbse secure login. Usernames and passwords are now encrypted when being sent from a user's computer to Xenbase.
• An image voting system to score images based on image quality
• To vote, click on an image of interest to bring up an enlarged view. Near the bottom of the popup are two icons, a thumbs up and a thumbs down, along with a comment box. Simply click one of the two icons to cast your vote. The user's choice is saved so it may be changed at a later date.
• Created a data statistics page for Xenbase which lists counts for various data types by year.
• Added a Sequence tab to gene pages which list associated mRNA and EST sequences.
• Added new tracks to the Xenbase Genome Browser.
• EcRs for mouse, zebrafish and chicken
• Promoter regions for tropicalis
• Xenopus tropicalis genomic fosmids
• JGI 4.1 tropicalis gene and transcript model sets
• Xenopus stage development time / temperature charts have been added.
• Exact searches added for select literature queries.
• Clone name searches will now except partial matches.
• In the stockcentre, users can now copy a transgene under a new name.
• Xenbase movies have been added to Youtube so they no longer have to be viewed in Quicktime.

Release 2.6.1

• Ability to add, edit, and delete clones.
• Stockcentre now supports transgenes.

Release 2.6

• Xenopus wiki for community contributions of protocols, gene information, etc.
• New version of Gbrowse (2.0.5) including tracks for: Unigene, Gurdon EST, cDNA clones and methylation
• Clone vector pages, including the ability to search clones by clone ID
• Clone, Vector and Library pages now have unique Xenbase accessions for searching
• Old Xenbase and XMMR have been decommissioned.

Release 2.5.5

• Search for clones via Gene symbol, NCBI accession, library name or clone name.
• Search for gene expression patterns by sequence.
• Search literature by Granting Agency or Grant Number
• New Xenbase cDNA library pages accessible through clone pages and gene expression search results
• Filter out ubiquitously expressed genes from gene expression search results
• Include Anatomical successor and predessor tissues in gene expression searches involving anatomy terms

Release 2.5

• Search Expression Patterns: Search Xenopus expression patterns by gene symbol, developmental stages, anatomical structures and experimenters
• Search gene pages by NCBI sequence accession for mRNA, EST and protein.

Release 2.4

• Search 'All': Search all of Xenbase from the minibar at the top of the screen
• Search suggestion ability added to mini bar for searches in: gene, person, lab, organization, authors and titles
• Expanded and updated Stockcenter for searching Xenopus frog lines
• Faster BLAST searches and new search databases added
• Faster gene 'Search All' searches
• Search genes by Affymetrix probe ID
• Ensembl models listed in gene pages and gBrowse
• Gene page link to literature referencing 'morpholinos'
• Gene expression images from AxelDB now available in the 'Expression' tab on gene pages
• Added thousands of expression images from community labs: Zorn lab, Papalopulu lab
• Over one thousand additional expression images automatically curated from literature sources

Release 2.3.1

• Gene page interactants tab added. This tab lists genes that are co-cited in the literature for a gene of interest.
• JGI Xentr4.1 filtered model transcript and protein databases are now available at the Xenbase blast site.

Release 2.3

• Animal lines section added. This section provides information on frog lines currently carried by the European Xenopus Resource Center (EXRC).

Release 2.2

• Gene pages are being populated with archetypal image(s) of gene expression patterns
• New Expression tab on Gene pages
  • in situ images from XDB3 (presence of images is indicated by an icon on the Expression tab). Axeldb and community submitted images available soon.
  • Anatomy terms and stages (expression data derived from EST/cDNA library representation). This is available for most genes even when they lack images.
• UniProt Knowledgebase links (alternative splicing information, protein domains and much more)
• Microarray data from GEO - view array data where the gene of interest displays differential expression
• Affymetrix probe sets for both trop and laevis
• Gene search
  • Select number of results per page
• Literature section
  • Publications with figures are flagged with a small icon. Load the paper to see the abstract, figures and legends, or click on the icon to see only the figures and legends.

Release 2.1

• Dramatically faster gene search and gene pages
• Literature tab added to gene page
• In-line links from article abstracts, titles and image captions to gene pages
• Improved gene search
  • Now search shows how results were found
  • New search by gene function

Release 2.01

• Addition of 7,600 + Metazome-curated gene models.