TY - JOUR
T1 - Mapping circulating serum miRNAs to their immune-related target mRNAs
AU - Nosirov, Bakhtiyor
AU - Billaud, Joël
AU - Vandenbon, Alexis
AU - Diez, Diego
AU - Wijaya, Edward
AU - Ishii, Ken J.
AU - Teraguchi, Shunsuke
AU - Standley, Daron M.
N1 - Publisher Copyright:
© 2017 Nosirov et al.
PY - 2017
Y1 - 2017
N2 - Purpose: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than nonserum miRNAs. Materials and methods: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA-mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). Results: Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. Conclusion: Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA-immune mRNA interactions than would be expected by chance.
AB - Purpose: Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than nonserum miRNAs. Materials and methods: We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA-mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). Results: Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. Conclusion: Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA-immune mRNA interactions than would be expected by chance.
KW - Biomarker
KW - Posttranscriptional regulation
KW - Random forest
KW - Target prediction
UR - http://www.scopus.com/inward/record.url?scp=85014654909&partnerID=8YFLogxK
U2 - 10.2147/AABC.S121598
DO - 10.2147/AABC.S121598
M3 - Article
AN - SCOPUS:85014654909
SN - 1178-6949
VL - 10
SP - 1
EP - 9
JO - Advances and Applications in Bioinformatics and Chemistry
JF - Advances and Applications in Bioinformatics and Chemistry
IS - 1
ER -