Dataset Information

26 mouse ES EB samples affymetrix exon array (affymetrix exon array)

ABSTRACT: Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied.

ORGANISM(S): Mus musculus

PROVIDER: GSE27397 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA136995

REPOSITORIES: GEO

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Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this study, we analyzed 26 mouse samples using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this Series, we analyzed 81 human leukemia samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

Dataset Information

26 mouse ES EB samples affymetrix exon array (affymetrix exon array)

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