ArticleBMC bioinformatics2007
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Broad and diverse mechanisms used by deubiquitinase family members in regulating the type I interferon signaling pathway during antiviral responses.Science advances · 2018Article
- A 35-gene signature discriminates between rapidly- and slowly-progressing glioblastoma multiforme and predicts survival in known subtypes of the cancer.BMC cancer · 2018Article
- Hemophagocytic Lymphohistocytosis in the Chinese Han Population May Be Associated with an STXBP2 Gene Polymorphism.PloS one · 2016Article
- SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.Molecular & cellular proteomics : MCP · 2014Article
- TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.BMC genomics · 2013Article
- The E3-ligase TRIM family of proteins regulates signaling pathways triggered by innate immune pattern-recognition receptors.Immunity · 2013Article
- Function of alternative splicing.Gene · 2013Review
- SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.Bioinformatics (Oxford, England) · 2012Article
- SpliceDisease database: linking RNA splicing and disease.Nucleic acids research · 2012Article
- Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors.Cancer research · 2010Article
- Single molecule analysis of combinatorial splicing.Nucleic acids research · 2010Article
- Ontogenomic study of the relationship between number of gene splice variants and GO categorization.Bioinformatics (Oxford, England) · 2010Article
- Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.PloS one · 2009Article
- SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.BMC bioinformatics · 2008Article
- Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets.BMC genomics · 2007Article
- Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundThere are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels. DESCRIPTION: SpliceMiner is a web interface for querying Evidence Viewer Database (EVDB). EVDB is a comprehensive, non-redundant compendium of splice variant data for human genes. We constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV). EVDB is based on data obtained from NCBI Entrez Gene and EV. The automated EVDB build process uses only complete coding sequences, which may or may not include partial or complete 5' and 3' UTRs, and filters redundant splice variants. Unlike EV, which supports only one-at-a-time queries, SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format. SpliceMiner maps probes to splice variants, effectively delineating the variants identified by a probe.
conclusionEVDB can be queried by gene symbol, genomic coordinates, or probe sequence via a user-friendly web-based tool we call SpliceMiner (http://discover.nci.nih.gov/spliceminer). The EVDB/SpliceMiner combination provides an interface with human splice variant information and, going beyond the very valuable NCBI Evidence Viewer, supports fluent, high-throughput analysis. Integration of EVDB information into microarray analysis and design pipelines has the potential to improve the analysis and bioinformatic interpretation of gene expression data, for both batch and interactive processing. For example, whenever a gene expression value is recognized as important or appears anomalous in a microarray experiment, the interactive mode of SpliceMiner can be used quickly and easily to check for possible splice variant issues.
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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.