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Long noncoding RNA associated-competing endogenous RNAs in gastric cancer
Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic...
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| Published in: | Scientific reports 2014-08, Vol.4 (1), p.6088, Article 6088 |
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| description | Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4 and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p and miR-195-5p) were involved. For instance, through its miRNA response elements (MREs) to compete for miR-106a-5p, lncRNA-FER1L4 regulates the expression of PTEN, RB1, RUNX1, VEGFA, CDKN1A, E2F1, HIPK3, IL-10 and PAK7. Furthermore, cellular experimental results indicated that FER1L4-small interfering RNA (siRNA) simultaneously suppressed FER1L4 and RB1 mRNA level. These results suggest that lncRNAs harbor MREs and play important roles in post-transcriptional regulation in cancer. |
| doi_str_mv | 10.1038/srep06088 |
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However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4 and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p and miR-195-5p) were involved. For instance, through its miRNA response elements (MREs) to compete for miR-106a-5p, lncRNA-FER1L4 regulates the expression of PTEN, RB1, RUNX1, VEGFA, CDKN1A, E2F1, HIPK3, IL-10 and PAK7. Furthermore, cellular experimental results indicated that FER1L4-small interfering RNA (siRNA) simultaneously suppressed FER1L4 and RB1 mRNA level. These results suggest that lncRNAs harbor MREs and play important roles in post-transcriptional regulation in cancer.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep06088</identifier><identifier>PMID: 25124853</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38 ; 38/61 ; 38/77 ; 692/699/67/1504/1829 ; 692/699/67/69 ; Algorithms ; Carcinoma - genetics ; Carcinoma, Papillary ; Carcinoma, Squamous Cell - genetics ; Cell Line, Tumor ; Cell Transformation, Neoplastic - genetics ; Chronic lymphocytic leukemia ; DNA microarrays ; Female ; Gastric cancer ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic - genetics ; Gene regulation ; Head & neck cancer ; Head and Neck Neoplasms - genetics ; Humanities and Social Sciences ; Humans ; Interleukin 10 ; Leukemia ; Leukemia, Lymphocytic, Chronic, B-Cell - genetics ; Lymphatic leukemia ; Male ; MicroRNAs - genetics ; miRNA ; multidisciplinary ; Oligonucleotide Array Sequence Analysis ; Ovarian cancer ; Ovarian Neoplasms - genetics ; Papillary thyroid carcinoma ; Pituitary ; Pituitary (anterior) ; Pituitary Neoplasms - genetics ; Post-transcription ; Prostate cancer ; Prostatic Neoplasms - genetics ; PTEN protein ; Regulatory sequences ; Retinoblastoma Protein - biosynthesis ; Retinoblastoma Protein - genetics ; RNA Interference ; RNA, Long Noncoding - genetics ; RNA, Small Interfering ; Runx1 protein ; Science ; siRNA ; Squamous cell carcinoma ; Squamous Cell Carcinoma of Head and Neck ; Stomach Neoplasms - genetics ; Thyroid ; Thyroid Cancer, Papillary ; Thyroid Neoplasms - genetics ; Transcription ; Tumors</subject><ispartof>Scientific reports, 2014-08, Vol.4 (1), p.6088, Article 6088</ispartof><rights>The Author(s) 2014</rights><rights>Copyright Nature Publishing Group Aug 2014</rights><rights>Copyright © 2014, Macmillan Publishers Limited. All rights reserved 2014 Macmillan Publishers Limited. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c544t-ea82af2256056bc9ed5b7b347442b408bfb893cf8638e039022b74b60d2fa7f43</citedby><cites>FETCH-LOGICAL-c544t-ea82af2256056bc9ed5b7b347442b408bfb893cf8638e039022b74b60d2fa7f43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1898118211/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1898118211?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25124853$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xia, Tian</creatorcontrib><creatorcontrib>Liao, Qi</creatorcontrib><creatorcontrib>Jiang, Xiaoming</creatorcontrib><creatorcontrib>Shao, Yongfu</creatorcontrib><creatorcontrib>Xiao, Bingxiu</creatorcontrib><creatorcontrib>Xi, Yang</creatorcontrib><creatorcontrib>Guo, Junming</creatorcontrib><title>Long noncoding RNA associated-competing endogenous RNAs in gastric cancer</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4 and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p and miR-195-5p) were involved. For instance, through its miRNA response elements (MREs) to compete for miR-106a-5p, lncRNA-FER1L4 regulates the expression of PTEN, RB1, RUNX1, VEGFA, CDKN1A, E2F1, HIPK3, IL-10 and PAK7. Furthermore, cellular experimental results indicated that FER1L4-small interfering RNA (siRNA) simultaneously suppressed FER1L4 and RB1 mRNA level. These results suggest that lncRNAs harbor MREs and play important roles in post-transcriptional regulation in cancer.</description><subject>38</subject><subject>38/61</subject><subject>38/77</subject><subject>692/699/67/1504/1829</subject><subject>692/699/67/69</subject><subject>Algorithms</subject><subject>Carcinoma - genetics</subject><subject>Carcinoma, Papillary</subject><subject>Carcinoma, Squamous Cell - genetics</subject><subject>Cell Line, Tumor</subject><subject>Cell Transformation, Neoplastic - genetics</subject><subject>Chronic lymphocytic leukemia</subject><subject>DNA microarrays</subject><subject>Female</subject><subject>Gastric cancer</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic - genetics</subject><subject>Gene regulation</subject><subject>Head & neck cancer</subject><subject>Head and Neck Neoplasms - genetics</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Interleukin 10</subject><subject>Leukemia</subject><subject>Leukemia, Lymphocytic, Chronic, B-Cell - genetics</subject><subject>Lymphatic leukemia</subject><subject>Male</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>multidisciplinary</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Ovarian cancer</subject><subject>Ovarian Neoplasms - genetics</subject><subject>Papillary thyroid carcinoma</subject><subject>Pituitary</subject><subject>Pituitary (anterior)</subject><subject>Pituitary Neoplasms - genetics</subject><subject>Post-transcription</subject><subject>Prostate cancer</subject><subject>Prostatic Neoplasms - genetics</subject><subject>PTEN protein</subject><subject>Regulatory sequences</subject><subject>Retinoblastoma Protein - biosynthesis</subject><subject>Retinoblastoma Protein - genetics</subject><subject>RNA Interference</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Small Interfering</subject><subject>Runx1 protein</subject><subject>Science</subject><subject>siRNA</subject><subject>Squamous cell carcinoma</subject><subject>Squamous Cell Carcinoma of Head and Neck</subject><subject>Stomach Neoplasms - genetics</subject><subject>Thyroid</subject><subject>Thyroid Cancer, Papillary</subject><subject>Thyroid Neoplasms - genetics</subject><subject>Transcription</subject><subject>Tumors</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNplkN1LwzAUxYMobsw9-A9IwSeFaj7b9EUYw4_BUBB9Dkma1o4tqUkr-N-bsjkm3pd74fw493AAOEfwBkHCb4M3Lcwg50dgjCFlKSYYHx_cIzANYQXjMFxQVJyCEWYIU87IGCyWztaJdVa7sonX6_MskSE43cjOlKl2m9Z0g2Bs6WpjXR8GJiSNTWoZOt_oREurjT8DJ5VcBzPd7Ql4f7h_mz-ly5fHxXy2TDWjtEuN5FhWGLMMskzpwpRM5YrQnFKsKOSqUrwguuIZ4QaSAmKscqoyWOJK5hUlE3C39W17tTGlNrbzci1a32yk_xZONuKvYpsPUbsvQREhOSyiweXOwLvP3oROrFzvbcwsEC84QhwjFKmrLaW9C7Hjav8BQTEUL_bFR_biMNKe_K05AtdbIETJ1sYfvPzn9gNjxIy1</recordid><startdate>20140815</startdate><enddate>20140815</enddate><creator>Xia, Tian</creator><creator>Liao, Qi</creator><creator>Jiang, Xiaoming</creator><creator>Shao, Yongfu</creator><creator>Xiao, Bingxiu</creator><creator>Xi, Yang</creator><creator>Guo, Junming</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>5PM</scope></search><sort><creationdate>20140815</creationdate><title>Long noncoding RNA associated-competing endogenous RNAs in gastric cancer</title><author>Xia, Tian ; Liao, Qi ; Jiang, Xiaoming ; Shao, Yongfu ; Xiao, Bingxiu ; Xi, Yang ; Guo, Junming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c544t-ea82af2256056bc9ed5b7b347442b408bfb893cf8638e039022b74b60d2fa7f43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>38</topic><topic>38/61</topic><topic>38/77</topic><topic>692/699/67/1504/1829</topic><topic>692/699/67/69</topic><topic>Algorithms</topic><topic>Carcinoma - genetics</topic><topic>Carcinoma, Papillary</topic><topic>Carcinoma, Squamous Cell - genetics</topic><topic>Cell Line, Tumor</topic><topic>Cell Transformation, Neoplastic - genetics</topic><topic>Chronic lymphocytic leukemia</topic><topic>DNA microarrays</topic><topic>Female</topic><topic>Gastric cancer</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Neoplastic - genetics</topic><topic>Gene regulation</topic><topic>Head & neck cancer</topic><topic>Head and Neck Neoplasms - genetics</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Interleukin 10</topic><topic>Leukemia</topic><topic>Leukemia, Lymphocytic, Chronic, B-Cell - genetics</topic><topic>Lymphatic leukemia</topic><topic>Male</topic><topic>MicroRNAs - genetics</topic><topic>miRNA</topic><topic>multidisciplinary</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Ovarian cancer</topic><topic>Ovarian Neoplasms - genetics</topic><topic>Papillary thyroid carcinoma</topic><topic>Pituitary</topic><topic>Pituitary (anterior)</topic><topic>Pituitary Neoplasms - genetics</topic><topic>Post-transcription</topic><topic>Prostate cancer</topic><topic>Prostatic Neoplasms - genetics</topic><topic>PTEN protein</topic><topic>Regulatory sequences</topic><topic>Retinoblastoma Protein - biosynthesis</topic><topic>Retinoblastoma Protein - genetics</topic><topic>RNA Interference</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Small Interfering</topic><topic>Runx1 protein</topic><topic>Science</topic><topic>siRNA</topic><topic>Squamous cell carcinoma</topic><topic>Squamous Cell Carcinoma of Head and Neck</topic><topic>Stomach Neoplasms - genetics</topic><topic>Thyroid</topic><topic>Thyroid Cancer, Papillary</topic><topic>Thyroid Neoplasms - genetics</topic><topic>Transcription</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xia, Tian</creatorcontrib><creatorcontrib>Liao, Qi</creatorcontrib><creatorcontrib>Jiang, Xiaoming</creatorcontrib><creatorcontrib>Shao, Yongfu</creatorcontrib><creatorcontrib>Xiao, Bingxiu</creatorcontrib><creatorcontrib>Xi, Yang</creatorcontrib><creatorcontrib>Guo, Junming</creatorcontrib><collection>SpringerOpen</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>ProQuest Biological Science Journals</collection><collection>Publicly Available Content Database (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xia, Tian</au><au>Liao, Qi</au><au>Jiang, Xiaoming</au><au>Shao, Yongfu</au><au>Xiao, Bingxiu</au><au>Xi, Yang</au><au>Guo, Junming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Long noncoding RNA associated-competing endogenous RNAs in gastric cancer</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2014-08-15</date><risdate>2014</risdate><volume>4</volume><issue>1</issue><spage>6088</spage><pages>6088-</pages><artnum>6088</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4 and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p and miR-195-5p) were involved. For instance, through its miRNA response elements (MREs) to compete for miR-106a-5p, lncRNA-FER1L4 regulates the expression of PTEN, RB1, RUNX1, VEGFA, CDKN1A, E2F1, HIPK3, IL-10 and PAK7. Furthermore, cellular experimental results indicated that FER1L4-small interfering RNA (siRNA) simultaneously suppressed FER1L4 and RB1 mRNA level. These results suggest that lncRNAs harbor MREs and play important roles in post-transcriptional regulation in cancer.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>25124853</pmid><doi>10.1038/srep06088</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 38 38/61 38/77 692/699/67/1504/1829 692/699/67/69 Algorithms Carcinoma - genetics Carcinoma, Papillary Carcinoma, Squamous Cell - genetics Cell Line, Tumor Cell Transformation, Neoplastic - genetics Chronic lymphocytic leukemia DNA microarrays Female Gastric cancer Gene expression Gene Expression Profiling Gene Expression Regulation, Neoplastic - genetics Gene regulation Head & neck cancer Head and Neck Neoplasms - genetics Humanities and Social Sciences Humans Interleukin 10 Leukemia Leukemia, Lymphocytic, Chronic, B-Cell - genetics Lymphatic leukemia Male MicroRNAs - genetics miRNA multidisciplinary Oligonucleotide Array Sequence Analysis Ovarian cancer Ovarian Neoplasms - genetics Papillary thyroid carcinoma Pituitary Pituitary (anterior) Pituitary Neoplasms - genetics Post-transcription Prostate cancer Prostatic Neoplasms - genetics PTEN protein Regulatory sequences Retinoblastoma Protein - biosynthesis Retinoblastoma Protein - genetics RNA Interference RNA, Long Noncoding - genetics RNA, Small Interfering Runx1 protein Science siRNA Squamous cell carcinoma Squamous Cell Carcinoma of Head and Neck Stomach Neoplasms - genetics Thyroid Thyroid Cancer, Papillary Thyroid Neoplasms - genetics Transcription Tumors |
| title | Long noncoding RNA associated-competing endogenous RNAs in gastric cancer |
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