ArticleNucleic acids research2018
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 129 citations in OpenAlex.
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- Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline.EMBO reports · 2024Article
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- Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona.Nature communications · 2024Article
- A Novel Hemocyte-Derived Peptide and Its Possible Roles in Immune Response ofInternational journal of molecular sciences · 2024Article
- Gene expression and cellular changes in injured myocardium ofFrontiers in cell and developmental biology · 2024Article
- Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling.PLoS biology · 2024Article
- Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage.Developmental biology · 2023Article
- De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus.G3 (Bethesda, Md.) · 2023Article
- Phylogenetic tracing of midbrain-specific regulatory sequences suggests single origin of eubilaterian brains.Science advances · 2023Article
- Model of neural induction in the ascidian embryo.PLoS computational biology · 2023Article
- Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis.Frontiers in bioinformatics · 2023Article
- New putative phenol oxidase in ascidian blood cells.Scientific reports · 2022Article
- RSAT 2022: regulatory sequence analysis tools.Nucleic acids research · 2022Article
- Highly distinct genetic programs for peripheral nervous system formation in chordates.BMC biology · 2022Article
- Article
Corrections and comments
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Authors and funding
39 authors at 14 institutions in 5 countries.
Funding
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.