Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.
Figure 1. Interactive RNA-Seq visualization. After selecting the central panel for X. laevis temporal data on a Gene Page ‘Expression’ tab, a larger window with additional controls opens as shown. A second gene, chordin, was added to further customize the view as described in the main text. Note that the noggin profile (purple) has been rescaled on the Y axis to accommodate the higher level of transcription of the chordin gene (red).
Figure 2. GO terms associated with an X. laevis and X. tropicalis gene.
Figure 3. Comparison of Xenopus literature gene co-citation to human protein interaction data from IntAct. A. Genes co-cited with axin1 in Xenbase. Two key interactants, ctnnb1 (beta-catenin, 10 co-citations) and gsk3b (glycogen synthase kinase 3 beta, 8 co-citations) are circled in red. B. IntAct data on human proteins interacting with AXIN1. CTNNB1 has 35 results and GSK3B has 41 results, ranging from co-immunoprecipitation and yeast two-hybrid interactions, to fluorescence polarization spectroscopy and protein kinase assays (click on interactions hyperlink on Xenbase to view evidence).
Figure 4. ORFeome page associated with an X. laevis gene.
Ahmed,
A Database of microRNA Expression Patterns in Xenopus laevis.
2015, Pubmed,
Xenbase
Ahmed,
A Database of microRNA Expression Patterns in Xenopus laevis.
2015,
Pubmed
,
Xenbase
Amberger,
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.
2015,
Pubmed
Antin,
GEISHA: an evolving gene expression resource for the chicken embryo.
2014,
Pubmed
Barrett,
NCBI GEO: archive for functional genomics data sets--update.
2013,
Pubmed
Blake,
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse.
2017,
Pubmed
Bowes,
Xenbase: a Xenopus biology and genomics resource.
2008,
Pubmed
,
Xenbase
Brown,
The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping.
2012,
Pubmed
Carbon,
AmiGO: online access to ontology and annotation data.
2009,
Pubmed
Cock,
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.
2010,
Pubmed
Diez-Roux,
A high-resolution anatomical atlas of the transcriptome in the mouse embryo.
2011,
Pubmed
Ding,
Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis.
2017,
Pubmed
,
Xenbase
Ernst,
ChromHMM: automating chromatin-state discovery and characterization.
2012,
Pubmed
Firth,
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
2009,
Pubmed
Gramates,
FlyBase at 25: looking to the future.
2017,
Pubmed
Grant,
The Xenopus ORFeome: A resource that enables functional genomics.
2015,
Pubmed
,
Xenbase
Grant,
FIMO: scanning for occurrences of a given motif.
2011,
Pubmed
Hawrylycz,
An anatomically comprehensive atlas of the adult human brain transcriptome.
2012,
Pubmed
Hermjakob,
IntAct: an open source molecular interaction database.
2004,
Pubmed
Hoffman,
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
2012,
Pubmed
Hontelez,
Embryonic transcription is controlled by maternally defined chromatin state.
2015,
Pubmed
,
Xenbase
Howe,
WormBase 2016: expanding to enable helminth genomic research.
2016,
Pubmed
James-Zorn,
Xenbase: expansion and updates of the Xenopus model organism database.
2013,
Pubmed
,
Xenbase
James-Zorn,
Xenbase: Core features, data acquisition, and data processing.
2015,
Pubmed
,
Xenbase
Kalderimis,
InterMine: extensive web services for modern biology.
2014,
Pubmed
Kanehisa,
KEGG: new perspectives on genomes, pathways, diseases and drugs.
2017,
Pubmed
Karimi,
The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.
2014,
Pubmed
,
Xenbase
Karpinka,
Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.
2015,
Pubmed
,
Xenbase
Kent,
BigWig and BigBed: enabling browsing of large distributed datasets.
2010,
Pubmed
Matsuda,
A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis.
2015,
Pubmed
,
Xenbase
Nemudryi,
TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery.
2014,
Pubmed
Oh,
A mesoscale connectome of the mouse brain.
2014,
Pubmed
Owens,
Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.
2016,
Pubmed
,
Xenbase
Quinlan,
BEDTools: a flexible suite of utilities for comparing genomic features.
2010,
Pubmed
Rappaport,
MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases.
2014,
Pubmed
Reid,
XenMine: A genomic interaction tool for the Xenopus community.
2017,
Pubmed
,
Xenbase
Segerdell,
An ontology for Xenopus anatomy and development.
2008,
Pubmed
,
Xenbase
Session,
Genome evolution in the allotetraploid frog Xenopus laevis.
2016,
Pubmed
,
Xenbase
Skinner,
JBrowse: a next-generation genome browser.
2009,
Pubmed
Stein,
The generic genome browser: a building block for a model organism system database.
2002,
Pubmed
Thomas,
PANTHER: a library of protein families and subfamilies indexed by function.
2003,
Pubmed
Tyner,
The UCSC Genome Browser database: 2017 update.
2017,
Pubmed
Uhlén,
Proteomics. Tissue-based map of the human proteome.
2015,
Pubmed
UniProt Consortium,
UniProt: a hub for protein information.
2015,
Pubmed
Vize,
Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase.
2015,
Pubmed
,
Xenbase
Vize,
Xenopus genomic data and browser resources.
2017,
Pubmed
,
Xenbase
Weirauch,
Determination and inference of eukaryotic transcription factor sequence specificity.
2014,
Pubmed
Yates,
Ensembl 2016.
2016,
Pubmed