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Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)
MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between mult...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275156/ https://www.ncbi.nlm.nih.gov/pubmed/18208839 http://dx.doi.org/10.1093/nar/gkm1165 |
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author | Lee, Inhan Ajay, Subramanian S. Chen, Haiming Maruyama, Atsushi Wang, Nulang McInnis, Melvin G. Athey, Brian D. |
author_facet | Lee, Inhan Ajay, Subramanian S. Chen, Haiming Maruyama, Atsushi Wang, Nulang McInnis, Melvin G. Athey, Brian D. |
author_sort | Lee, Inhan |
collection | PubMed |
description | MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray “signal” probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform. |
format | Text |
id | pubmed-2275156 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-22751562008-04-07 Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) Lee, Inhan Ajay, Subramanian S. Chen, Haiming Maruyama, Atsushi Wang, Nulang McInnis, Melvin G. Athey, Brian D. Nucleic Acids Res Methods Online MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray “signal” probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform. Oxford University Press 2008-03 2008-01-21 /pmc/articles/PMC2275156/ /pubmed/18208839 http://dx.doi.org/10.1093/nar/gkm1165 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Lee, Inhan Ajay, Subramanian S. Chen, Haiming Maruyama, Atsushi Wang, Nulang McInnis, Melvin G. Athey, Brian D. Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title_full | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title_fullStr | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title_full_unstemmed | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title_short | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
title_sort | discriminating single-base difference mirna expressions using microarray probe design guru (prodeg) |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275156/ https://www.ncbi.nlm.nih.gov/pubmed/18208839 http://dx.doi.org/10.1093/nar/gkm1165 |
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