title: XenMine: A genomic interaction tool for the Xenopus community.
abstract: The Xenopus community has embraced recent advances in sequencing technology, resulting in the accumulation of numerous RNA-Seq and ChIP-Seq datasets. However, easily accessing and comparing datasets generated by multiple laboratories is challenging. Thus, we have created a central space to view, search and analyze data, providing essential information on gene expression changes and regulatory elements present in the genome. XenMine (www.xenmine.org) is a user-friendly website containing published genomic datasets from both Xenopus tropicalis and Xenopus laevis. We have established an analysis pipeline where all published datasets are uniformly processed with the latest genome releases. Information from these datasets can be extracted and compared using an array of pre-built or custom templates. With these search tools, users can easily extract sequences for all putative regulatory domains surrounding a gene of interest, identify the expression values of a gene of interest over developmental time, and analyze lists of genes for gene ontology terms and publications. Additionally, XenMine hosts an in-house genome browser that allows users to visualize all available ChIP-Seq data, extract specifically marked sequences, and aid in identifying important regulatory elements within the genome. Altogether, XenMine is an excellent tool for visualizing, accessing and querying analyzed datasets rapidly and efficiently.
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Christine D
authors.initials: CD
authors.lastname: Reid
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Karra
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Chang
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Piskol
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: Jin Billy
authors.initials: JB
authors.lastname: Li
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
authors.affiliation: Department of Genetics, Stanford University, Stanford CA 94305, USA. Electronic address: jbaker@stanford.edu.
authors.forename: Julie C
authors.initials: JC
authors.lastname: Baker
mesh_terms: D000818:Animals; D001483:Base Sequence; D057225:Data Mining; D030541:Databases, Genetic; D066264:Datasets as Topic; D015870:Gene Expression; D063990:Gene Ontology; D016678:Genome; D023281:Genomics / Q000379:methods*; D020407:Internet; D012313:RNA / Q000096:biosynthesis / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014981:Xenopus / Q000235:genetics*
chemical_list: D012313:RNA