TY - GEN
T1 - In silico prediction of target SNPs affecting miR-mRNA interaction
AU - Sun, Hao
AU - Nicoloso, Milena S.
AU - Bhattacharyya, Anirban
AU - Calin, George A.
AU - Davuluri, Ramana V.
PY - 2008
Y1 - 2008
N2 - MicroRNAs (miRs) are a large family of short 20-25-nt single-stranded noncoding RNAs, recently identified in many eukaryotes from nematode to human, which play an important role in gene regulation. Single nucleotide polymorphisms (SNPs) are the most common genetic variants in the human genome, and an immense source of information for localizing and identifying disease susceptible genes. Here, we investigate how the SNPs located in transcribed regions of protein coding genes will affect the miR-mRNA interaction by altering the Minimum Free Energy (MFE) of the miR-mRNA duplex, thus destroying the existing miR target sites or creating the new target sites. We propose that a combination of multiple allelic variants in miR target regions can alter the gene regulation and contribute to the likelihood of disease development. We developed a bioinformatics pipeline to predict the target SNPs, which can potentially influence the miR-mRNA interaction, based on the SNPs' ability to alter the MFE of the miR-mRNA duplex. We annotated and integrated such target SNPs, miRs, and the target gene annotation information into an integrated database, called miR-SNPDB (http://bioinformatics.wistar.upenn.edu/mir-snpdb) as a public resource for research community.
AB - MicroRNAs (miRs) are a large family of short 20-25-nt single-stranded noncoding RNAs, recently identified in many eukaryotes from nematode to human, which play an important role in gene regulation. Single nucleotide polymorphisms (SNPs) are the most common genetic variants in the human genome, and an immense source of information for localizing and identifying disease susceptible genes. Here, we investigate how the SNPs located in transcribed regions of protein coding genes will affect the miR-mRNA interaction by altering the Minimum Free Energy (MFE) of the miR-mRNA duplex, thus destroying the existing miR target sites or creating the new target sites. We propose that a combination of multiple allelic variants in miR target regions can alter the gene regulation and contribute to the likelihood of disease development. We developed a bioinformatics pipeline to predict the target SNPs, which can potentially influence the miR-mRNA interaction, based on the SNPs' ability to alter the MFE of the miR-mRNA duplex. We annotated and integrated such target SNPs, miRs, and the target gene annotation information into an integrated database, called miR-SNPDB (http://bioinformatics.wistar.upenn.edu/mir-snpdb) as a public resource for research community.
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U2 - 10.1109/BIBMW.2008.4686238
DO - 10.1109/BIBMW.2008.4686238
M3 - Conference contribution
AN - SCOPUS:58049158649
SN - 9781424428908
T3 - Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
SP - 211
EP - 214
BT - Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
T2 - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
Y2 - 3 November 2008 through 5 November 2008
ER -
