Xenbase Release Notes
- Minor enhancements and bug fixes
- Redesigned site for improved look and feel
- New site is now responsive to mobile devices
- Added announcements carousel to landing page for promoting high impact Xenpous research, Xenopus researchers, and new Xenopus research technologies
- Added antibodies database
- New GBrowse server and software (2.55). New tracks added
- Added antibody pages and search interface
- Added protein tab to gene pages
- Summary images on gene page summary auto-rotate
- 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
- 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.
- Xenbase 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.
- Ability to add, edit, and delete clones.
- Stockcentre now supports transgenes.
- 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.
- 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
- 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.
- 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
- 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.
- Animal lines section added. This section provides information on frog lines currently carried by the European Xenopus Resource Center (EXRC).
- 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.
- 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
- Addition of 7,600 + Metazome-curated gene models.