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In this review, we describe the recent advances in studying cancer-associated... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_5474451" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes from a systems biological point of view. The integration of known cancer genes onto protein and signaling networks reveals the characteristics of cancer genes within networks. This approach shows that cancer genes often function as network hub proteins which are involved in many cellular processes and form focal nodes in the information exchange between many signaling pathways. Literature mining allows constructing gene-gene networks, in which new cancer genes can be identified. The gene expression profiles of cancer cells are used for reconstructing gene regulatory networks. 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Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="5400" href="https://www.academia.edu/Documents/in/Systems_Biology">Systems Biology</a>, <script data-card-contents-for-ri="5400" type="text/json">{"id":5400,"name":"Systems Biology","url":"https://www.academia.edu/Documents/in/Systems_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="210852" href="https://www.academia.edu/Documents/in/Gene_Regulatory_Networks">Gene Regulatory Networks</a><script data-card-contents-for-ri="210852" type="text/json">{"id":210852,"name":"Gene Regulatory Networks","url":"https://www.academia.edu/Documents/in/Gene_Regulatory_Networks","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=5474499]'), work: {"id":5474499,"title":"Network motifs are enriched with transcription 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class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/5474500/Aberrant_allele_frequencies_of_the_SNPs_located_in_microRNA_target_sites_are_potentially_associated_with_human_cancers">Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers</a></div></div><div class="u-pb4x u-mt3x"></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/5474500" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="b41ed74da0c1645f363043db0ff18717" rel="nofollow" data-download="{"attachment_id":32589054,"asset_id":5474500,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/32589054/download_file?st=MTczMjQ3NDAzNCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="7692962" href="https://nrc-ca.academia.edu/EdwinWang">Edwin Wang</a><script data-card-contents-for-user="7692962" 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window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-percentile-work_5474500"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></li><li class="js-view-count-work_5474500 InlineList-item InlineList-item--bordered hidden"><div><span><span class="js-view-count view-count u-mr2x" data-work-id="5474500"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 5474500; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=5474500]").text(description); $(".js-view-count-work_5474500").attr('title', description).tooltip(); }); });</script></span><script>$(function() { $(".js-view-count-work_5474500").removeClass('hidden') })</script></div></li><li class="InlineList-item u-positionRelative" style="max-width: 250px"><div class="u-positionAbsolute" data-has-card-for-ri-list="5474500"><i class="fa fa-tag InlineList-item-icon u-positionRelative"></i>  <a class="InlineList-item-text u-positionRelative">4</a>  </div><span class="InlineList-item-text u-textTruncate u-pl9x"><a class="InlineList-item-text" data-has-card-for-ri="5490" href="https://www.academia.edu/Documents/in/MicroRNA">MicroRNA</a>, <script data-card-contents-for-ri="5490" type="text/json">{"id":5490,"name":"MicroRNA","url":"https://www.academia.edu/Documents/in/MicroRNA","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="6021" href="https://www.academia.edu/Documents/in/Cancer">Cancer</a>, <script data-card-contents-for-ri="6021" type="text/json">{"id":6021,"name":"Cancer","url":"https://www.academia.edu/Documents/in/Cancer","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="52523" href="https://www.academia.edu/Documents/in/miRNA">miRNA</a>, <script data-card-contents-for-ri="52523" type="text/json">{"id":52523,"name":"miRNA","url":"https://www.academia.edu/Documents/in/miRNA","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="58317" href="https://www.academia.edu/Documents/in/SNP_associated_genomics">SNP associated genomics</a><script data-card-contents-for-ri="58317" type="text/json">{"id":58317,"name":"SNP associated genomics","url":"https://www.academia.edu/Documents/in/SNP_associated_genomics","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=5474500]'), work: {"id":5474500,"title":"Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human 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Wang","profile_url":"https://nrc-ca.academia.edu/EdwinWang","photo":"/images/s65_no_pic.png"}],"research_interests":[{"id":5490,"name":"MicroRNA","url":"https://www.academia.edu/Documents/in/MicroRNA","nofollow":false},{"id":6021,"name":"Cancer","url":"https://www.academia.edu/Documents/in/Cancer","nofollow":false},{"id":52523,"name":"miRNA","url":"https://www.academia.edu/Documents/in/miRNA","nofollow":false},{"id":58317,"name":"SNP associated genomics","url":"https://www.academia.edu/Documents/in/SNP_associated_genomics","nofollow":false}],"publication_year":2007,"publication_year_with_fallback":2007,"paper_rank":null,"all_time_views":66,"active_discussion":{}}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_5474502" data-work_id="5474502" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/5474502/MicroRNA_Systems_Biology">MicroRNA Systems Biology</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_5474502" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is challenging the central dogma of molecular biology. Genes are working together by forming cellular networks. It has become an emerging concept that miRNAs could intertwine with cellular networks to exert their function. Thus, it is essential to understand how miRNAs take part in cellular processes at a systems-level. In this review, I will first introduce basic knowledge of miRNAs and their relations to heart disaeses and cancer, highlight recently dicovered functions such as filtering out gene expression noise by miRNAs. I will aslo introduce basic concepts of cellular networks and interpret their biological meaning in such a way that the network concepts are digested in a biological context and are understandable for biologists. Finally, I will summarize the most recent progress in understanding of miRNA biology at a systems-level: the principles of miRNA regulation of the major cellular networks including signaling, metabolic, protein interaction and gene regulatory networks. A common miRNA regulatory principle is emerging: miRNAs preferentially regulated the genes that have high regulation complexity. In addition, miRNAs preferentially regulate positive regulatory motifs, highly connected scaffolds and the most network downstream components of cellular signaling networks, while miRNAs selectively regulate the genes which have specific network structural features on metabolic networks.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/5474502" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="2f706ed345335342500faf91c3741897" rel="nofollow" data-download="{"attachment_id":32589056,"asset_id":5474502,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/32589056/download_file?st=MTczMjQ3NDAzNCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="7692962" href="https://nrc-ca.academia.edu/EdwinWang">Edwin Wang</a><script data-card-contents-for-user="7692962" type="text/json">{"id":7692962,"first_name":"Edwin","last_name":"Wang","domain_name":"nrc-ca","page_name":"EdwinWang","display_name":"Edwin Wang","profile_url":"https://nrc-ca.academia.edu/EdwinWang","photo":"/images/s65_no_pic.png"}</script></span></span></li><li class="js-paper-rank-work_5474502 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="5474502"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 5474502, container: ".js-paper-rank-work_5474502", }); 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$(".js-view-count[data-work-id=5474502]").text(description); $(".js-view-count-work_5474502").attr('title', description).tooltip(); }); });</script></span><script>$(function() { $(".js-view-count-work_5474502").removeClass('hidden') })</script></div></li><li class="InlineList-item u-positionRelative" style="max-width: 250px"><div class="u-positionAbsolute" data-has-card-for-ri-list="5474502"><i class="fa fa-tag InlineList-item-icon u-positionRelative"></i>  <a class="InlineList-item-text u-positionRelative">5</a>  </div><span class="InlineList-item-text u-textTruncate u-pl9x"><a class="InlineList-item-text" data-has-card-for-ri="146" href="https://www.academia.edu/Documents/in/Bioinformatics">Bioinformatics</a>, <script data-card-contents-for-ri="146" type="text/json">{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="4233" href="https://www.academia.edu/Documents/in/Computational_Biology">Computational Biology</a>, <script data-card-contents-for-ri="4233" type="text/json">{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="5400" href="https://www.academia.edu/Documents/in/Systems_Biology">Systems Biology</a>, <script data-card-contents-for-ri="5400" type="text/json">{"id":5400,"name":"Systems Biology","url":"https://www.academia.edu/Documents/in/Systems_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="5490" href="https://www.academia.edu/Documents/in/MicroRNA">MicroRNA</a><script data-card-contents-for-ri="5490" type="text/json">{"id":5490,"name":"MicroRNA","url":"https://www.academia.edu/Documents/in/MicroRNA","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=5474502]'), work: {"id":5474502,"title":"MicroRNA Systems Biology","created_at":"2013-12-18T18:27:39.282-08:00","owner_id":7692962,"url":"https://www.academia.edu/5474502/MicroRNA_Systems_Biology","slug":"MicroRNA_Systems_Biology","dom_id":"work_5474502","summary":"Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is challenging the central dogma of molecular biology. Genes are working together by forming cellular networks. It has become an emerging concept that miRNAs could intertwine with cellular networks to exert their function. Thus, it is essential to understand how miRNAs take part in cellular processes at a systems-level. In this review, I will first introduce basic knowledge of miRNAs and their relations to heart disaeses and cancer, highlight recently dicovered functions such as filtering out gene expression noise by miRNAs. I will aslo introduce basic concepts of cellular networks and interpret their biological meaning in such a way that the network concepts are digested in a biological context and are understandable for biologists. Finally, I will summarize the most recent progress in understanding of miRNA biology at a systems-level: the principles of miRNA regulation of the major cellular networks including signaling, metabolic, protein interaction and gene regulatory networks. A common miRNA regulatory principle is emerging: miRNAs preferentially regulated the genes that have high regulation complexity. In addition, miRNAs preferentially regulate positive regulatory motifs, highly connected scaffolds and the most network downstream components of cellular signaling networks, while miRNAs selectively regulate the genes which have specific network structural features on metabolic networks.","publication":null,"publication_with_fallback":"arXiv (Cornell University)","downloadable_attachments":[{"id":32589056,"asset_id":5474502,"asset_type":"Work","always_allow_download":false,"scribd_thumbnail_url":"https://attachments.academia-assets.com/32589056/thumbnails/1.jpg","download_url":"https://d1wqtxts1xzle7.cloudfront.net/32589056/0712.3569-libre.pdf?1391137995=\u0026response-content-disposition=attachment%3B+filename%3DMicroRNA_Systems_Biology.pdf\u0026Expires=1732193660\u0026Signature=ZeRyI6suMUNxP7-j5HirdtgsNdVhy~LKnlysqjtVW47BfWfeBETg3wCFE-GtoVaO3V1owSsmnYUEgJRHpZs~quRKnZQ92WM0adWEt60VqtadfZWpOcTnc00gfyq1afhkt9mJLgAUjFG5o~JIWRLd8hw203x3Ls1ND4W35jsIxO8n005u~7ymNeQs5V13YQO6cf2zZEgcxBsjfncVxN1u3Zvp5hjBbBw-jsrB2gLv3D8a2702gH8-pkfQjFJl0x7HMTv60l15PPvtP2Uvp6bK3TzkQPAED70V5SrDkLrjdcDuUrWol3-~WcYukL0L4U6g2MXZSkvdIQVAAyqd-S5yqQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA","download_file_url":"https://www.academia.edu/attachments/32589056/download_file?st=MTczMjQ3NDAzNCw4LjIyMi4yMDguMTQ2&","full_thumbnail_url":"https://0.academia-photos.com/attachment_thumbnails/32589056/mini_magick20190414-6224-rpie2a.png?1555281565"}],"downloadable_attachments_with_full_thumbnails":[{"id":32589056,"asset_id":5474502,"asset_type":"Work","always_allow_download":false,"scribd_thumbnail_url":"https://attachments.academia-assets.com/32589056/thumbnails/1.jpg","download_url":"https://d1wqtxts1xzle7.cloudfront.net/32589056/0712.3569-libre.pdf?1391137995=\u0026response-content-disposition=attachment%3B+filename%3DMicroRNA_Systems_Biology.pdf\u0026Expires=1732193660\u0026Signature=ZeRyI6suMUNxP7-j5HirdtgsNdVhy~LKnlysqjtVW47BfWfeBETg3wCFE-GtoVaO3V1owSsmnYUEgJRHpZs~quRKnZQ92WM0adWEt60VqtadfZWpOcTnc00gfyq1afhkt9mJLgAUjFG5o~JIWRLd8hw203x3Ls1ND4W35jsIxO8n005u~7ymNeQs5V13YQO6cf2zZEgcxBsjfncVxN1u3Zvp5hjBbBw-jsrB2gLv3D8a2702gH8-pkfQjFJl0x7HMTv60l15PPvtP2Uvp6bK3TzkQPAED70V5SrDkLrjdcDuUrWol3-~WcYukL0L4U6g2MXZSkvdIQVAAyqd-S5yqQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA","download_file_url":"https://www.academia.edu/attachments/32589056/download_file?st=MTczMjQ3NDAzNCw4LjIyMi4yMDguMTQ2&","full_thumbnail_url":"https://0.academia-photos.com/attachment_thumbnails/32589056/mini_magick20190414-6224-rpie2a.png?1555281565"}],"has_pdf":true,"has_fulltext":true,"page_count":39,"ordered_authors":[{"id":7692962,"first_name":"Edwin","last_name":"Wang","domain_name":"nrc-ca","page_name":"EdwinWang","display_name":"Edwin Wang","profile_url":"https://nrc-ca.academia.edu/EdwinWang","photo":"/images/s65_no_pic.png"}],"research_interests":[{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics","nofollow":false},{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology","nofollow":false},{"id":5400,"name":"Systems Biology","url":"https://www.academia.edu/Documents/in/Systems_Biology","nofollow":false},{"id":5490,"name":"MicroRNA","url":"https://www.academia.edu/Documents/in/MicroRNA","nofollow":false},{"id":52523,"name":"miRNA","url":"https://www.academia.edu/Documents/in/miRNA"}],"publication_year":2007,"publication_year_with_fallback":2007,"paper_rank":null,"all_time_views":70,"active_discussion":{}}, }) } })();</script></ul></li></ul></div></div><div class="u-borderBottom1 u-borderColorGrayLighter"><div class="clearfix u-pv7x u-mb0x js-work-card work_5474577" data-work_id="5474577" itemscope="itemscope" itemtype="https://schema.org/ScholarlyArticle"><div class="header"><div class="title u-fontSerif u-fs22 u-lineHeight1_3"><a class="u-tcGrayDarkest js-work-link" href="https://www.academia.edu/5474577/microRNA_evolution_in_a_human_transcription_factor_and_microRNA_regulatory_network">microRNA evolution in a human transcription factor and microRNA regulatory network</a></div></div><div class="u-pb4x u-mt3x"><div class="summary u-fs14 u-fw300 u-lineHeight1_5 u-tcGrayDarkest"><div class="summarized">Background microRNAs (miRNAs) are important cellular components. The understanding of their evolution is of critical importance for the understanding of their function. Although some specific evolutionary rules of miRNAs have been... <a class="more_link u-tcGrayDark u-linkUnstyled" data-container=".work_5474577" data-show=".complete" data-hide=".summarized" data-more-link-behavior="true" href="#">more</a></div><div class="complete hidden">Background microRNAs (miRNAs) are important cellular components. The understanding of their evolution is of critical importance for the understanding of their function. Although some specific evolutionary rules of miRNAs have been revealed, the rules of miRNA evolution in cellular networks remain largely unexplored. According to knowledge from protein-coding genes, the investigations of gene evolution in the context of biological networks often generate valuable observations that cannot be obtained by traditional approaches. Results Here, we conducted the first systems-level analysis of miRNA evolution in a human transcription factor (TF)-miRNA regulatory network that describes the regulatory relations among TFs, miRNAs, and target genes. We found that the architectural structure of the network provides constraints and functional innovations for miRNA evolution and that miRNAs showed different and even opposite evolutionary patterns from TFs and other protein-coding genes. For example, miRNAs preferentially coevolved with their activators but not with their inhibitors. During transcription, rapidly evolving TFs frequently activated but rarely repressed miRNAs. In addition, conserved miRNAs tended to regulate rapidly evolving targets, and upstream miRNAs evolved more rapidly than downstream miRNAs. Conclusions In this study, we performed the first systems level analysis of miRNA evolution. The findings suggest that miRNAs have a unique evolution process and thus may have unique functions and roles in various biological processes and diseases. Additionally, the network presented here is the first TF-miRNA regulatory network, which will be a valuable platform of systems biology.</div></div></div><ul class="InlineList u-ph0x u-fs13"><li class="InlineList-item logged_in_only"><div class="share_on_academia_work_button"><a class="academia_share Button Button--inverseBlue Button--sm js-bookmark-button" data-academia-share="Work/5474577" data-share-source="work_strip" data-spinner="small_white_hide_contents"><i class="fa fa-plus"></i><span class="work-strip-link-text u-ml1x" data-content="button_text">Bookmark</span></a></div></li><li class="InlineList-item"><div class="download"><a id="5852d2030ae99ce332eed6ee94187d5f" rel="nofollow" data-download="{"attachment_id":49278605,"asset_id":5474577,"asset_type":"Work","always_allow_download":false,"track":null,"button_location":"work_strip","source":null,"hide_modal":null}" class="Button Button--sm Button--inverseGreen js-download-button prompt_button doc_download" href="https://www.academia.edu/attachments/49278605/download_file?st=MTczMjQ3NDAzNCw4LjIyMi4yMDguMTQ2&s=work_strip"><i class="fa fa-arrow-circle-o-down fa-lg"></i><span class="u-textUppercase u-ml1x" data-content="button_text">Download</span></a></div></li><li class="InlineList-item"><ul class="InlineList InlineList--bordered u-ph0x"><li class="InlineList-item InlineList-item--bordered"><span class="InlineList-item-text">by <span itemscope="itemscope" itemprop="author" itemtype="https://schema.org/Person"><a class="u-tcGrayDark u-fw700" data-has-card-for-user="7692962" href="https://nrc-ca.academia.edu/EdwinWang">Edwin Wang</a><script data-card-contents-for-user="7692962" type="text/json">{"id":7692962,"first_name":"Edwin","last_name":"Wang","domain_name":"nrc-ca","page_name":"EdwinWang","display_name":"Edwin Wang","profile_url":"https://nrc-ca.academia.edu/EdwinWang","photo":"/images/s65_no_pic.png"}</script></span></span></li><li class="js-paper-rank-work_5474577 InlineList-item InlineList-item--bordered hidden"><span class="js-paper-rank-view hidden u-tcGrayDark" data-paper-rank-work-id="5474577"><i class="u-m1x fa fa-bar-chart"></i><strong class="js-paper-rank"></strong></span><script>$(function() { new Works.PaperRankView({ workId: 5474577, container: ".js-paper-rank-work_5474577", }); 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$(".js-view-count[data-work-id=5474577]").text(description); $(".js-view-count-work_5474577").attr('title', description).tooltip(); }); });</script></span><script>$(function() { $(".js-view-count-work_5474577").removeClass('hidden') })</script></div></li><li class="InlineList-item u-positionRelative" style="max-width: 250px"><div class="u-positionAbsolute" data-has-card-for-ri-list="5474577"><i class="fa fa-tag InlineList-item-icon u-positionRelative"></i>  <a class="InlineList-item-text u-positionRelative">5</a>  </div><span class="InlineList-item-text u-textTruncate u-pl9x"><a class="InlineList-item-text" data-has-card-for-ri="146" href="https://www.academia.edu/Documents/in/Bioinformatics">Bioinformatics</a>, <script data-card-contents-for-ri="146" type="text/json">{"id":146,"name":"Bioinformatics","url":"https://www.academia.edu/Documents/in/Bioinformatics","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="155" href="https://www.academia.edu/Documents/in/Evolutionary_Biology">Evolutionary Biology</a>, <script data-card-contents-for-ri="155" type="text/json">{"id":155,"name":"Evolutionary Biology","url":"https://www.academia.edu/Documents/in/Evolutionary_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="4233" href="https://www.academia.edu/Documents/in/Computational_Biology">Computational Biology</a>, <script data-card-contents-for-ri="4233" type="text/json">{"id":4233,"name":"Computational Biology","url":"https://www.academia.edu/Documents/in/Computational_Biology","nofollow":false}</script><a class="InlineList-item-text" data-has-card-for-ri="5400" href="https://www.academia.edu/Documents/in/Systems_Biology">Systems Biology</a><script data-card-contents-for-ri="5400" type="text/json">{"id":5400,"name":"Systems Biology","url":"https://www.academia.edu/Documents/in/Systems_Biology","nofollow":false}</script></span></li><script>(function(){ if (true) { new Aedu.ResearchInterestListCard({ el: $('*[data-has-card-for-ri-list=5474577]'), work: {"id":5474577,"title":"microRNA evolution in a human transcription factor and microRNA regulatory network","created_at":"2013-12-18T18:36:33.327-08:00","owner_id":7692962,"url":"https://www.academia.edu/5474577/microRNA_evolution_in_a_human_transcription_factor_and_microRNA_regulatory_network","slug":"microRNA_evolution_in_a_human_transcription_factor_and_microRNA_regulatory_network","dom_id":"work_5474577","summary":"Background microRNAs (miRNAs) are important cellular components. The understanding of their evolution is of critical importance for the understanding of their function. Although some specific evolutionary rules of miRNAs have been revealed, the rules of miRNA evolution in cellular networks remain largely unexplored. According to knowledge from protein-coding genes, the investigations of gene evolution in the context of biological networks often generate valuable observations that cannot be obtained by traditional approaches. Results Here, we conducted the first systems-level analysis of miRNA evolution in a human transcription factor (TF)-miRNA regulatory network that describes the regulatory relations among TFs, miRNAs, and target genes. We found that the architectural structure of the network provides constraints and functional innovations for miRNA evolution and that miRNAs showed different and even opposite evolutionary patterns from TFs and other protein-coding genes. For example, miRNAs preferentially coevolved with their activators but not with their inhibitors. During transcription, rapidly evolving TFs frequently activated but rarely repressed miRNAs. In addition, conserved miRNAs tended to regulate rapidly evolving targets, and upstream miRNAs evolved more rapidly than downstream miRNAs. Conclusions In this study, we performed the first systems level analysis of miRNA evolution. The findings suggest that miRNAs have a unique evolution process and thus may have unique functions and roles in various biological processes and diseases. Additionally, the network presented here is the first TF-miRNA regulatory network, which will be a valuable platform of systems biology.","publication":"BMC Systems Biology","publication_with_fallback":"BMC Systems 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