ArticleBMC bioinformatics2016
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea.Proceedings. Biological sciences · 2023Article
- EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms.BMC genomic data · 2022Article
- A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.Genome biology and evolution · 2022Article
- Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record.eLife · 2022Article
- A nomenclature for echinoderm genes.Database : the journal of biological databases and curation · 2021Article
- Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge.BMC genomics · 2020Article
- Automated gene data integration with Databio.BMC research notes · 2020Article
- Sea Urchin as a Universal Model for Studies of Gene Networks.Frontiers in genetics · 2020Review
- A phylogenomic resolution of the sea urchin tree of life.BMC evolutionary biology · 2018Article
- Decimation by sea star wasting disease and rapid genetic change in a keystone species,Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution.Genome biology · 2018Article
- A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence.Open biology · 2017Article
- Workflow and web application for annotating NCBI BioProject transcriptome data.Database : the journal of biological databases and curation · 2017Article
- Regeneration in bipinnaria larvae of the bat star Patiria miniata induces rapid and broad new gene expression.Mechanisms of development · 2016Article
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9 authors.
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Abstract
backgroundOne of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinoderm phylogeny and transcriptomics. We used RNA-Seq to profile adult tissues from 42 echinoderm specimens from 24 orders and 37 families. In order to achieve sampling members of clades that span key evolutionary divergence, many of our exemplars were collected from deep and polar seas. DESCRIPTION: A small fraction of the transcriptome data we produced is being used for phylogenetic reconstruction. Thus to make a larger dataset available to researchers with a wide variety of interests, we made a web-based application, EchinoDB (http://echinodb.uncc.edu). EchinoDB is a repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity.
conclusionsFrom transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology.
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