Identification and analysis of novel microRNAs from fragile sites of human cervical cancer: Computational and experimental approach
Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool ‘Mpred’ which first identifies pre-miRNAs and then predicts its mature miRNAs. We first use our method to...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2011-06, Vol.97 (6), p.333-340 |
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| creator | Reshmi, G. Chandra, S.S. Vinod Babu, V. Janki Mohan Babu, P.S. Saneesh Santhi, W.S. Ramachandran, Surya Lakshmi, S. Nair, Achuthsankar S. Pillai, M. Radhakrishna |
| description | Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool ‘Mpred’ which first identifies pre-miRNAs and then predicts its mature miRNAs. We first use our method to learn with high accuracy characteristic features of human miRNA precursors from miRbase registry and then apply to sequences from fragile site regions related to cervical cancer in search of novel miRNA genes. The study identified 13 putative miRNA-like sequences and most of them were not related to each other and do not share homology with annotated sequences. Finally, four of the top scoring predictions were verified experimentally using quantitative RT-PCR validation. Expression profile studies revealed that four novel miRs were present in cervical tissues and these data compiled here provide a regulatory framework of miRNA genes that may have roles in tumorigenesis. |
| doi_str_mv | 10.1016/j.ygeno.2011.02.010 |
| format | Article |
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Vinod ; Babu, V. Janki Mohan ; Babu, P.S. Saneesh ; Santhi, W.S. ; Ramachandran, Surya ; Lakshmi, S. ; Nair, Achuthsankar S. ; Pillai, M. Radhakrishna</creator><creatorcontrib>Reshmi, G. ; Chandra, S.S. Vinod ; Babu, V. Janki Mohan ; Babu, P.S. Saneesh ; Santhi, W.S. ; Ramachandran, Surya ; Lakshmi, S. ; Nair, Achuthsankar S. ; Pillai, M. Radhakrishna</creatorcontrib><description>Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool ‘Mpred’ which first identifies pre-miRNAs and then predicts its mature miRNAs. We first use our method to learn with high accuracy characteristic features of human miRNA precursors from miRbase registry and then apply to sequences from fragile site regions related to cervical cancer in search of novel miRNA genes. The study identified 13 putative miRNA-like sequences and most of them were not related to each other and do not share homology with annotated sequences. Finally, four of the top scoring predictions were verified experimentally using quantitative RT-PCR validation. Expression profile studies revealed that four novel miRs were present in cervical tissues and these data compiled here provide a regulatory framework of miRNA genes that may have roles in tumorigenesis.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2011.02.010</identifier><identifier>PMID: 21377523</identifier><language>eng</language><publisher>Amsterdam: Elsevier Inc</publisher><subject>Artificial Intelligence ; Artificial neural network ; Base Sequence ; Biological and medical sciences ; carcinogenesis ; Cell Line, Tumor ; Cervical cancer ; Computer Simulation ; Female ; Female genital diseases ; Fragile sites ; Fundamental and applied biological sciences. Psychology ; Gene Expression Regulation, Neoplastic ; genes ; Genes. Genome ; Genetic Association Studies ; Genetics of eukaryotes. Biological and molecular evolution ; Gynecology. Andrology. Obstetrics ; Hidden Markov model ; Humans ; Markov Chains ; Medical sciences ; microRNA ; MicroRNAs ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Models, Genetic ; Molecular and cellular biology ; Molecular genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; prediction ; Quantitative real-time PCR ; reverse transcriptase polymerase chain reaction ; ROC Curve ; Software ; Tumors ; uterine cervical neoplasms ; Uterine Cervical Neoplasms - genetics ; Uterine Cervical Neoplasms - metabolism</subject><ispartof>Genomics (San Diego, Calif.), 2011-06, Vol.97 (6), p.333-340</ispartof><rights>2011 Elsevier Inc.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2011 Elsevier Inc. 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Vinod</creatorcontrib><creatorcontrib>Babu, V. Janki Mohan</creatorcontrib><creatorcontrib>Babu, P.S. Saneesh</creatorcontrib><creatorcontrib>Santhi, W.S.</creatorcontrib><creatorcontrib>Ramachandran, Surya</creatorcontrib><creatorcontrib>Lakshmi, S.</creatorcontrib><creatorcontrib>Nair, Achuthsankar S.</creatorcontrib><creatorcontrib>Pillai, M. Radhakrishna</creatorcontrib><title>Identification and analysis of novel microRNAs from fragile sites of human cervical cancer: Computational and experimental approach</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool ‘Mpred’ which first identifies pre-miRNAs and then predicts its mature miRNAs. 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Expression profile studies revealed that four novel miRs were present in cervical tissues and these data compiled here provide a regulatory framework of miRNA genes that may have roles in tumorigenesis.</description><subject>Artificial Intelligence</subject><subject>Artificial neural network</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>carcinogenesis</subject><subject>Cell Line, Tumor</subject><subject>Cervical cancer</subject><subject>Computer Simulation</subject><subject>Female</subject><subject>Female genital diseases</subject><subject>Fragile sites</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>genes</subject><subject>Genes. Genome</subject><subject>Genetic Association Studies</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Gynecology. Andrology. Obstetrics</subject><subject>Hidden Markov model</subject><subject>Humans</subject><subject>Markov Chains</subject><subject>Medical sciences</subject><subject>microRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Models, Genetic</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>prediction</subject><subject>Quantitative real-time PCR</subject><subject>reverse transcriptase polymerase chain reaction</subject><subject>ROC Curve</subject><subject>Software</subject><subject>Tumors</subject><subject>uterine cervical neoplasms</subject><subject>Uterine Cervical Neoplasms - genetics</subject><subject>Uterine Cervical Neoplasms - metabolism</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUuP0zAUhSMEYsrAL0CCbBCrBDt-xEaaxajiMdIIJGDWluPcdFwlcbGTiq7549y0BXaw8ENX3z3XPifLnlNSUkLlm2152MAYyopQWpKqJJQ8yFaUKF0oyeXDbEWUUkUtOLvInqS0JYRopqrH2UVFWV2Liq2ynzctjJPvvLOTD2NuxxaX7Q_Jpzx0-Rj20OeDdzF8-XSd8i6GATe78T3kyU9wpO7nwY65g7hHnT53dsT723wdht08HYWxukjDjx1EP-DIpbDbxWDd_dPsUWf7BM_O52V29_7dt_XH4vbzh5v19W3huNJTYWuubEsrW0OlKy46Sp0TrqON7JgUxNa6kqLhjZaM6YZrJ6jtrFWSEBAg2GX2-qSLY7_PkCYz-OSg7-0IYU5GaU05qRn9Pyk1J1IqhSQ7kWhQShE6s8P_2XgwlJglJrM1x5jMEpMhlcGYsOvFWX9uBmj_9PzOBYFXZ8AmdBQNH51PfznOmMBckXt54jobjN1EZO6-4iSBWXM8F-LqRAA6u_cQTXIeMJ_WR3CTaYP_51N_Ac-XvEw</recordid><startdate>20110601</startdate><enddate>20110601</enddate><creator>Reshmi, G.</creator><creator>Chandra, S.S. Vinod</creator><creator>Babu, V. Janki Mohan</creator><creator>Babu, P.S. Saneesh</creator><creator>Santhi, W.S.</creator><creator>Ramachandran, Surya</creator><creator>Lakshmi, S.</creator><creator>Nair, Achuthsankar S.</creator><creator>Pillai, M. Radhakrishna</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20110601</creationdate><title>Identification and analysis of novel microRNAs from fragile sites of human cervical cancer: Computational and experimental approach</title><author>Reshmi, G. ; Chandra, S.S. Vinod ; Babu, V. Janki Mohan ; Babu, P.S. Saneesh ; Santhi, W.S. ; Ramachandran, Surya ; Lakshmi, S. ; Nair, Achuthsankar S. ; Pillai, M. Radhakrishna</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c489t-a748ad12a7e29245f11cc5cf1b6f3650a79265b4b96339b49c51afaa8600e5e53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Artificial Intelligence</topic><topic>Artificial neural network</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>carcinogenesis</topic><topic>Cell Line, Tumor</topic><topic>Cervical cancer</topic><topic>Computer Simulation</topic><topic>Female</topic><topic>Female genital diseases</topic><topic>Fragile sites</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>genes</topic><topic>Genes. Genome</topic><topic>Genetic Association Studies</topic><topic>Genetics of eukaryotes. 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| subjects | Artificial Intelligence Artificial neural network Base Sequence Biological and medical sciences carcinogenesis Cell Line, Tumor Cervical cancer Computer Simulation Female Female genital diseases Fragile sites Fundamental and applied biological sciences. Psychology Gene Expression Regulation, Neoplastic genes Genes. Genome Genetic Association Studies Genetics of eukaryotes. Biological and molecular evolution Gynecology. Andrology. Obstetrics Hidden Markov model Humans Markov Chains Medical sciences microRNA MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism Models, Genetic Molecular and cellular biology Molecular genetics Molecular Sequence Data Nucleic Acid Conformation prediction Quantitative real-time PCR reverse transcriptase polymerase chain reaction ROC Curve Software Tumors uterine cervical neoplasms Uterine Cervical Neoplasms - genetics Uterine Cervical Neoplasms - metabolism |
| title | Identification and analysis of novel microRNAs from fragile sites of human cervical cancer: Computational and experimental approach |
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