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...
Gespeichert in:
| Veröffentlicht in: | Nucleic acids research 2008-03, Vol.36 (5), p.e27-e27 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e27 |
|---|---|
| container_issue | 5 |
| container_start_page | e27 |
| container_title | Nucleic acids research |
| container_volume | 36 |
| creator | Lee, Inhan Ajay, Subramanian S Chen, Haiming Maruyama, Atsushi Wang, Nulang McInnis, Melvin G Athey, Brian D |
| 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. |
| doi_str_mv | 10.1093/nar/gkm1165 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2275156</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/nar/gkm1165</oup_id><sourcerecordid>70408998</sourcerecordid><originalsourceid>FETCH-LOGICAL-c605t-3ccb7d3229d3ed718fef8ca40113164a0478ab224ddf8bdd5fbf121dec8fb9a73</originalsourceid><addsrcrecordid>eNqFks1v1DAQxSMEokvhxB0iDgiEQv2V2LkgVV3YRar43EorLpYTj4PbxF7sBLX_PV7tqgUue7GlmZ-e_d5Mlj3F6C1GNT1xKpx0VwPGVXkvm2FakYLVFbmfzRBFZYERE0fZoxgvEcIMl-xhdoQFQULQepa1cxvbYAfr1Ghdl8d09FA0KkKurTEQwLWQD_bbp9McrjcBYrTexXzakqneBq9CUDf5l-AbyOcQbefyxRSm_FUqzWHx-nH2wKg-wpP9fZxdfHi_OlsW558XH89Oz4u2QuVY0LZtuKaE1JqC5lgYMKJVDGFMccUUYlyohhCmtRGN1qVpDCZYQytMUytOj7N3O93N1AygW3BjUL3cJHsq3EivrPy34-xP2fnfkhBe4rJKAi_3AsH_miCOckjpQN8rB36KkiOGRF2LgyCuK46qNJzDIOO0RNunX_wHXvopuBSXJCj1BSdbg292UAo9xgDm1htGcrsLMu2C3O9Cop_9Hccdux_-3ef8tDmgVOxAG0e4vkVVuJIVp7yUy_UP-XXFxXq-Wsp14p_veKO8VF2wUV58JwhThAQvac3oHziI12g</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>200638727</pqid></control><display><type>article</type><title>Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)</title><source>Oxford Journals Open Access Collection</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Lee, Inhan ; Ajay, Subramanian S ; Chen, Haiming ; Maruyama, Atsushi ; Wang, Nulang ; McInnis, Melvin G ; Athey, Brian D</creator><creatorcontrib>Lee, Inhan ; Ajay, Subramanian S ; Chen, Haiming ; Maruyama, Atsushi ; Wang, Nulang ; McInnis, Melvin G ; Athey, Brian D</creatorcontrib><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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkm1165</identifier><identifier>PMID: 18208839</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Algorithms ; Base Pair Mismatch ; Cell Line ; DNA, Complementary - analysis ; Gene Expression Profiling - methods ; Humans ; Methods Online ; MicroRNAs - analysis ; MicroRNAs - chemistry ; MicroRNAs - metabolism ; Nucleic Acid Denaturation ; Oligonucleotide Array Sequence Analysis - methods ; Oligonucleotide Probes - chemistry ; Reverse Transcriptase Polymerase Chain Reaction</subject><ispartof>Nucleic acids research, 2008-03, Vol.36 (5), p.e27-e27</ispartof><rights>2008 The Author(s) 2008</rights><rights>2008 The Author(s)</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c605t-3ccb7d3229d3ed718fef8ca40113164a0478ab224ddf8bdd5fbf121dec8fb9a73</citedby><cites>FETCH-LOGICAL-c605t-3ccb7d3229d3ed718fef8ca40113164a0478ab224ddf8bdd5fbf121dec8fb9a73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275156/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275156/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18208839$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Inhan</creatorcontrib><creatorcontrib>Ajay, Subramanian S</creatorcontrib><creatorcontrib>Chen, Haiming</creatorcontrib><creatorcontrib>Maruyama, Atsushi</creatorcontrib><creatorcontrib>Wang, Nulang</creatorcontrib><creatorcontrib>McInnis, Melvin G</creatorcontrib><creatorcontrib>Athey, Brian D</creatorcontrib><title>Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><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.</description><subject>Algorithms</subject><subject>Base Pair Mismatch</subject><subject>Cell Line</subject><subject>DNA, Complementary - analysis</subject><subject>Gene Expression Profiling - methods</subject><subject>Humans</subject><subject>Methods Online</subject><subject>MicroRNAs - analysis</subject><subject>MicroRNAs - chemistry</subject><subject>MicroRNAs - metabolism</subject><subject>Nucleic Acid Denaturation</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oligonucleotide Probes - chemistry</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqFks1v1DAQxSMEokvhxB0iDgiEQv2V2LkgVV3YRar43EorLpYTj4PbxF7sBLX_PV7tqgUue7GlmZ-e_d5Mlj3F6C1GNT1xKpx0VwPGVXkvm2FakYLVFbmfzRBFZYERE0fZoxgvEcIMl-xhdoQFQULQepa1cxvbYAfr1Ghdl8d09FA0KkKurTEQwLWQD_bbp9McrjcBYrTexXzakqneBq9CUDf5l-AbyOcQbefyxRSm_FUqzWHx-nH2wKg-wpP9fZxdfHi_OlsW558XH89Oz4u2QuVY0LZtuKaE1JqC5lgYMKJVDGFMccUUYlyohhCmtRGN1qVpDCZYQytMUytOj7N3O93N1AygW3BjUL3cJHsq3EivrPy34-xP2fnfkhBe4rJKAi_3AsH_miCOckjpQN8rB36KkiOGRF2LgyCuK46qNJzDIOO0RNunX_wHXvopuBSXJCj1BSdbg292UAo9xgDm1htGcrsLMu2C3O9Cop_9Hccdux_-3ef8tDmgVOxAG0e4vkVVuJIVp7yUy_UP-XXFxXq-Wsp14p_veKO8VF2wUV58JwhThAQvac3oHziI12g</recordid><startdate>20080301</startdate><enddate>20080301</enddate><creator>Lee, Inhan</creator><creator>Ajay, Subramanian S</creator><creator>Chen, Haiming</creator><creator>Maruyama, Atsushi</creator><creator>Wang, Nulang</creator><creator>McInnis, Melvin G</creator><creator>Athey, Brian D</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>FBQ</scope><scope>BSCLL</scope><scope>TOX</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>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20080301</creationdate><title>Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)</title><author>Lee, Inhan ; Ajay, Subramanian S ; Chen, Haiming ; Maruyama, Atsushi ; Wang, Nulang ; McInnis, Melvin G ; Athey, Brian D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c605t-3ccb7d3229d3ed718fef8ca40113164a0478ab224ddf8bdd5fbf121dec8fb9a73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Algorithms</topic><topic>Base Pair Mismatch</topic><topic>Cell Line</topic><topic>DNA, Complementary - analysis</topic><topic>Gene Expression Profiling - methods</topic><topic>Humans</topic><topic>Methods Online</topic><topic>MicroRNAs - analysis</topic><topic>MicroRNAs - chemistry</topic><topic>MicroRNAs - metabolism</topic><topic>Nucleic Acid Denaturation</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Oligonucleotide Probes - chemistry</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, Inhan</creatorcontrib><creatorcontrib>Ajay, Subramanian S</creatorcontrib><creatorcontrib>Chen, Haiming</creatorcontrib><creatorcontrib>Maruyama, Atsushi</creatorcontrib><creatorcontrib>Wang, Nulang</creatorcontrib><creatorcontrib>McInnis, Melvin G</creatorcontrib><creatorcontrib>Athey, Brian D</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, Inhan</au><au>Ajay, Subramanian S</au><au>Chen, Haiming</au><au>Maruyama, Atsushi</au><au>Wang, Nulang</au><au>McInnis, Melvin G</au><au>Athey, Brian D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2008-03-01</date><risdate>2008</risdate><volume>36</volume><issue>5</issue><spage>e27</spage><epage>e27</epage><pages>e27-e27</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>18208839</pmid><doi>10.1093/nar/gkm1165</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2008-03, Vol.36 (5), p.e27-e27 |
| issn | 0305-1048 1362-4962 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2275156 |
| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Base Pair Mismatch Cell Line DNA, Complementary - analysis Gene Expression Profiling - methods Humans Methods Online MicroRNAs - analysis MicroRNAs - chemistry MicroRNAs - metabolism Nucleic Acid Denaturation Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Probes - chemistry Reverse Transcriptase Polymerase Chain Reaction |
| title | Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T05%3A22%3A23IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Discriminating%20single-base%20difference%20miRNA%20expressions%20using%20microarray%20Probe%20Design%20Guru%20(ProDeG)&rft.jtitle=Nucleic%20acids%20research&rft.au=Lee,%20Inhan&rft.date=2008-03-01&rft.volume=36&rft.issue=5&rft.spage=e27&rft.epage=e27&rft.pages=e27-e27&rft.issn=0305-1048&rft.eissn=1362-4962&rft.coden=NARHAD&rft_id=info:doi/10.1093/nar/gkm1165&rft_dat=%3Cproquest_pubme%3E70408998%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=200638727&rft_id=info:pmid/18208839&rft_oup_id=10.1093/nar/gkm1165&rfr_iscdi=true |