ArticleBioinformatics (Oxford, England)2017
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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
19 citing papers in PubMed.
- Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression.NAR genomics and bioinformatics · 2023Article
- Article
- The miR-429 suppresses proliferation and migration in glioblastoma cells and induces cell-cycle arrest and apoptosis via modulating several target genes of ERBB signaling pathway.Molecular biology reports · 2022Article
- Tissue specific expression of UMAMIT amino acid transporters in wheat.Scientific reports · 2022Article
- Pan-phylumFrontiers in endocrinology · 2022Article
- Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data.PloS one · 2022Article
- Scripting Analyses of Genomes in Ensembl Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- recount3: summaries and queries for large-scale RNA-seq expression and splicing.Genome biology · 2021Article
- Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.Nature methods · 2021Article
- Article
- A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification.International journal of molecular sciences · 2020Article
- Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease.Patterns (New York, N.Y.) · 2020Article
- A bioinformatics analysis on the potential role of ACE2 in cardiac impairment of patients with coronavirus disease 2019.Annals of translational medicine · 2020Article
- Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies.International journal of molecular sciences · 2020Article
- Metric learning on expression data for gene function prediction.Bioinformatics (Oxford, England) · 2020Article
- AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species.BMC plant biology · 2018Article
- Cloud computing for genomic data analysis and collaboration.Nature reviews. Genetics · 2018Review
- Expression Atlas: gene and protein expression across multiple studies and organisms.Nucleic acids research · 2018Article
- A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwarfism in Chicken.Frontiers in genetics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer.
resultsThe RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. AVAILABILITY AND IMPLEMENTATION: The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api . The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library . CONTACT: rnaseq@ebi.ac.uk ; rpetry@ebi.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.