ArticlePloS one2013
Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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Who cites it
20 citing papers in PubMed.
- Targeted Next-Generation Sequencing in Rare Diseases.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Annotations of novel antennae-expressed genes in male Glossina morsitans morsitans tsetse flies.PloS one · 2022Article
- Analysis of Liver Responses to Non-alcoholic Steatohepatitis by mRNA-Sequencing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility.Animals : an open access journal from MDPI · 2021Article
- Sequencing error profiles of Illumina sequencing instruments.NAR genomics and bioinformatics · 2021Article
- Identification of KIF4A and its effect on the progression of lung adenocarcinoma based on the bioinformatics analysis.Bioscience reports · 2021Article
- Article
- Cannabidiol enhances cytotoxicity of anti-cancer drugs in human head and neck squamous cell carcinoma.Scientific reports · 2020Article
- High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications.Physical chemistry chemical physics : PCCP · 2020Review
- Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.BMC genomics · 2020Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
- Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan.Memorias do Instituto Oswaldo Cruz · 2020Article
- CXCL6 is an important paracrine factor in the pro-angiogenic human cardiac progenitor-like cell secretome.Scientific reports · 2017Article
- Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.GigaScience · 2017Article
- Data integration aids understanding of butterfly-host plant networks.Scientific reports · 2017Article
- The most common technologies and tools for functional genome analysis.Acta medica Lituanic · 2017Article
- DNApod: DNA polymorphism annotation database from next-generation sequence read archives.PloS one · 2017Article
- DFAST and DAGA: web-based integrated genome annotation tools and resources.Bioscience of microbiota, food and health · 2016Article
- Investigation into the annotation of protocol sequencing steps in the sequence read archive.GigaScience · 2015Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA.
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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.