Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant

Ari B Kahn1, Michael C Ryan, Hongfang Liu

  • 1Department of Bioinformatics, George Mason University, Fairfax, Virginia, USA. arik@mail.nih.gov <arik@mail.nih.gov>

BMC Bioinformatics
|March 7, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Photo-enhanced dehydrogenation of formic acid on Pd-based hybrid plasmonic nanostructures.

Nanoscale advances·2023
Same author

GRU-D-Weibull: A novel real-time individualized endpoint prediction.

Artificial intelligence in medicine·2023
Same author

Semi-spontaneous temporal evolution of relief/fluorescence hybrid gratings for holographic encryption.

Optics letters·2023
Same author

Correction: A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

BMC genomics·2023
Same author

Stratifying Future Stroke Risk with Incidentally- Discovered White Matter Disease Severity and Covert Brain Infarct Site.

Cerebrovascular diseases (Basel, Switzerland)·2023
Same author

Identification of endoplasmic reticulum stress-related biomarkers of diabetes nephropathy based on bioinformatics and machine learning.

Frontiers in endocrinology·2023

Alternative splicing generates diverse human transcripts from limited genes. SpliceMiner, a web tool querying the Evidence Viewer Database (EVDB), enables high-throughput analysis of splice variants, improving microarray data interpretation.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • The human genome contains fewer genes than expressed transcripts, primarily due to alternative splicing.
  • Alternative splicing produces tissue-specific, developmental stage-specific, and condition-specific transcripts.
  • Accurate analysis of microarray data and new array design for alternative splicing necessitate probe-level sequence and exon assessment.

Purpose of the Study:

  • To develop SpliceMiner, a web interface for querying the Evidence Viewer Database (EVDB).
  • To provide a comprehensive, non-redundant compendium of human splice variant data.
  • To enable high-throughput batch queries and facilitate probe-to-splice variant mapping.

Main Methods:

  • Constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV).

Related Experiment Videos

  • Utilized data from NCBI Entrez Gene and EV, filtering for complete coding sequences and non-redundant splice variants.
  • Developed SpliceMiner as a user-friendly web interface for querying EVDB by gene symbol, genomic coordinates, or probe sequence.

    • Main Results:

    • EVDB provides a comprehensive compendium of human splice variant data.
    • SpliceMiner supports high-throughput batch queries, unlike the single-query EV.
    • SpliceMiner effectively maps probes to specific splice variants.

    Conclusions:

    • The EVDB/SpliceMiner combination offers a powerful interface for human splice variant information.
    • This tool facilitates fluent, high-throughput analysis, enhancing the NCBI Evidence Viewer.
    • Integrating EVDB/SpliceMiner into microarray pipelines can improve gene expression data analysis and bioinformatic interpretation, aiding in the identification of splice variant issues.