ArticleNucleic acids research2020
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation.PLoS biology · 2024Pooled it
- Article
- Xenbase: A Guide to the Xenopus Genetics and Genomics Knowledgebase.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis.Mobile DNA · 2025Article
- Exploring therapeutic mechanism of Fuzhenghefuzhiyang Formula in psoriasis: inflammation and metabolism regulation.Frontiers in immunology · 2025Article
- Deletion upstream of MAB21L2 highlights the importance of evolutionarily conserved non-coding sequences for eye development.Nature communications · 2024Article
- Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates.G3 (Bethesda, Md.) · 2024Article
- Characterization of regeneration initiating cells during Xenopus laevis tail regeneration.Genome biology · 2024Article
- Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse.Genetics · 2024Article
- Using Xenopus to discover new candidate genes involved in BOR and other congenital hearing loss syndromes.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2024Review
- Modelling human genetic disorders in Xenopus tropicalis.Disease models & mechanisms · 2024Review
- Evidence for widespread cytoplasmic structuring into mesoscale condensates.Nature cell biology · 2024Article
- The sulfotransferase XB5850668.L is required to apportion embryonic ectodermal domains.Developmental dynamics : an official publication of the American Association of Anatomists · 2023Article
- Lysine deserts and cullin-RING ligase receptors: Navigating untrodden paths in proteostasis.iScience · 2023Article
- Embryonic and skeletal development of the albino African clawed frog (Xenopus laevis).Journal of anatomy · 2023Article
- Gene expression analysis of the Tao kinase family of Ste20p-like map kinase kinase kinases during early embryonic development in Xenopus laevis.Gene expression patterns : GEP · 2023Article
- The VGNC: expanding standardized vertebrate gene nomenclature.Genome biology · 2023Article
- Article
- The Gene Ontology knowledgebase in 2023.Genetics · 2023Review
- A single-cell, time-resolved profiling ofScience advances · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated 'gene expression as a phenotype' and gene regulatory network analyses.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.