Name
Abstract | ||
|---|---|---|
Splice junction microarrays and RNA-seq are two popular ways of quantifying splice variants within a cell. Unfortunately, isoform expressions cannot always be determined from the expressions of individual exons and splice junctions. While this issue has been noted before, the extent of the problem on various platforms has not yet been explored, nor have potential remedies been presented.We propose criteria that will guarantee identifiability of an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq. We show that up to 97% of 2256 alternatively spliced human genes selected from the RefSeq database lead to identifiable gene models in RNA-seq, with similar results in mouse. However, in the Human Exon array only 26% of these genes lead to identifiable models, and even in the most comprehensive splice junction array only 69% lead to identifiable models.Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/bioinformatics/btp544 | Bioinformatics |
Keywords | Field | DocType |
refseq database lead,identifiable gene model,comprehensive splice junction array,isoform deconvolution model,splice junction,splice junction microarrays,splice variant,human exon array,identifiable model,splice junction array,gene expression profiling,alternative splicing,gene selection,rna,computational biology | Gene isoform,RefSeq,splice,Identifiability,Computer science,Exon,Alternative splicing,Bioinformatics,Human genome,Genetics,DNA microarray | Journal |
Volume | Issue | ISSN |
25 | 23 | 1367-4811 |
Citations | PageRank | References |
10 | 1.17 | 6 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| David Hiller | 1 | 10 | 1.17 |
| Hui Jiang | 2 | 201 | 39.94 |
| Weihong Xu | 3 | 11 | 1.56 |
| Wing Hung Wong | 4 | 607 | 96.45 |