2016
DOI: 10.1093/nar/gkw263
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iGEMS: an integrated model for identification of alternative exon usage events

Abstract: DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high c… Show more

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Cited by 20 publications
(42 citation statements)
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“…For example, the mTOR amino acid sensing Ragulator complex gene, LAMTOR5 (Li et al, ), was down‐regulated from the third to sixth decade and densely associated with lncRNAs ( n = 22). Using blood gene expression data from monozygotic twins (Sood et al, ), we conducted pilot heritability analyses (Figure b, Table , and Figure ). Heritability of the age‐related gene expression—estimated from intraclass correlation analysis using blood RNA—was less for lncRNAs ( p = 2.2 × 10 −16 , mean difference: −0.2756 [95% CI: −0.2828, −0.2685]), compared with age‐related protein‐coding gene expression.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…For example, the mTOR amino acid sensing Ragulator complex gene, LAMTOR5 (Li et al, ), was down‐regulated from the third to sixth decade and densely associated with lncRNAs ( n = 22). Using blood gene expression data from monozygotic twins (Sood et al, ), we conducted pilot heritability analyses (Figure b, Table , and Figure ). Heritability of the age‐related gene expression—estimated from intraclass correlation analysis using blood RNA—was less for lncRNAs ( p = 2.2 × 10 −16 , mean difference: −0.2756 [95% CI: −0.2828, −0.2685]), compared with age‐related protein‐coding gene expression.…”
Section: Resultsmentioning
confidence: 99%
“…Additional modules included mitochondrial, endoplasmic reticulum, and ribonuclear proteins with ncRNA of unknown function closely integrated with these protein‐coding genes. (b) Intraclass correlations (ICCs) of age‐regulated genes as indicators of heritability plotted for noncoding and protein‐coding expression using HTA 2.0 blood RNA profiles obtained from 17 pairs of homozygotic twins (Sood et al, ). The heritability estimate was greater for protein‐coding genes ( p < 0.0001, See Table )…”
Section: Resultsmentioning
confidence: 99%
“…The development of exon microarrays enabled the transcriptomic study of differential splicing events, but PCR validation rates for identification of splice differences via microarray analysis tend to be lower than those observed for identification of differential gene expression using similar technologies [ 3 5 ]. Junction arrays [ 6 10 ] have been proposed to overcome this problem by using oligonucleotide probe-sets that interrogate junctions between exons in the transcriptome, as well as the exons themselves.…”
Section: Introductionmentioning
confidence: 99%
“…The development of exon microarrays enabled the transcriptomic study of differential splicing events, but PCR validation rates for identification of splice differences via microarray analysis tend to be lower than those observed for identification of differential gene expression using similar technologies [3][4][5]. Junction arrays [6][7][8][9][10] have been proposed to overcome this problem by using oligonucleotide probe-sets that interrogate junctions between exons in the transcriptome, as well as the exons themselves.…”
Section: Introductionmentioning
confidence: 99%