Transcriptomics,Genomics

Dataset Information

17

Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy


ABSTRACT: Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data. Overall design: Affymetrix HuEx1.0 ST exon array analysis of three control muscles and three myotonic dystrophy muscles

INSTRUMENT(S): [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]

SUBMITTER: Kinji Ohno  

PROVIDER: GSE18274 | GEO | 2013-09-05

SECONDARY ACCESSION(S): PRJNA117947

REPOSITORIES: GEO

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Publications

Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy.

Yamashita Yoshihiro Y   Matsuura Tohru T   Shinmi Jun J   Amakusa Yoshinobu Y   Masuda Akio A   Ito Mikako M   Kinoshita Masanobu M   Furuya Hirokazu H   Abe Koji K   Ibi Tohru T   Sahashi Ko K   Ohno Kinji K  

Journal of human genetics 20120419 6


Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and T  ...[more]

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