|
|
(10 intermediate revisions by 3 users not shown) |
Line 37: |
Line 37: |
| background-color:#e0e0e0;margin-top:1%;margin-bottom:20px;padding:20px;padding-top:40px; | | background-color:#e0e0e0;margin-top:1%;margin-bottom:20px;padding:20px;padding-top:40px; |
| } | | } |
| + | |
| + | #top_menu_inside, #top_menu_inside:before, #top_menu_inside:after { -webkit-box-sizing: content-box; -moz-box-sizing: border-box; box-sizing: content-box;} |
| + | #top_menu_under{font-size: 12px;} |
| + | #top_menu_14{font-size: 12px; height:18px} |
| + | #top_menu_inside li{font-size: 12px;} |
| + | #user_item{font-size: 12px;} |
| </style> | | </style> |
| </head> | | </head> |
Line 60: |
Line 66: |
| <div class="navbar-collapse collapse" style="padding-top:5px;padding-bottom:0"> | | <div class="navbar-collapse collapse" style="padding-top:5px;padding-bottom:0"> |
| <!-- Start Navigation List --> | | <!-- Start Navigation List --> |
− | <ul class="nav navbar-nav navbar-right " style="padding-bottom:15px;height:88px;padding-top:10px"> | + | <ul class="nav navbar-nav navbar-right " style="padding-bottom:15px;padding-top:10px"> |
| <li> | | <li> |
| <a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Achievements</a> | | <a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Achievements</a> |
Line 140: |
Line 146: |
| <div class="row"> | | <div class="row"> |
| <div class="col-md-6"> | | <div class="col-md-6"> |
− | <h2 style="font-size:20px; margin-bottom:5px; padding-bottom:0">Modeling</h2> | + | <h2 style="font-size:20px; margin-bottom:5px; padding-bottom:0">M<span style="text-transform:lowercase">odeling</span></h2> |
− | <p style="margin-top:0px;font-size:14px">The purpose of models is not to fit the data but to sharpen the questions. </p> | + | <p style="margin-top:0px;font-size:14px" id="Analysis-Background">The purpose of models is not to fit the data but to sharpen the questions. </p> |
| </div> | | </div> |
| <div class="col-md-6"> | | <div class="col-md-6"> |
Line 163: |
Line 169: |
| <!-- Sidebar for windows > 1024px --> | | <!-- Sidebar for windows > 1024px --> |
| <div id="sidebar1"class="widget widget-categories"> | | <div id="sidebar1"class="widget widget-categories"> |
− | <h4 style="font-size:18px">Marker Finder<span class="head-line"></span></h4> | + | <h4 style="font-size:18px">A<span style="text-transform:lowercase">nalysis Algorithm</span><span class="head-line"></span></h4> |
| <ul> | | <ul> |
| <li><a href="#Analysis-Background">Background</a></li> | | <li><a href="#Analysis-Background">Background</a></li> |
Line 172: |
Line 178: |
| <!-- Sidebar for windows < 1024px --> | | <!-- Sidebar for windows < 1024px --> |
| <div id="sidebar2"class="widget widget-categories"> | | <div id="sidebar2"class="widget widget-categories"> |
− | <h4 style="font-size:18px">Team <span class="head-line"></span></h4> | + | <h4 style="font-size:18px">A<span style="text-transform:lowercase">nalysis Algorithm</span><span class="head-line"></span></h4> |
| <ul> | | <ul> |
| <li><a href="#Analysis-Background">Background</a></li> | | <li><a href="#Analysis-Background">Background</a></li> |
Line 182: |
Line 188: |
| <!--End sidebar--> | | <!--End sidebar--> |
| <!-- Page Content --> | | <!-- Page Content --> |
− | <div class="col-md-9 page-content"> | + | <div class="col-md-9 page-content" style="text-align:justify;"> |
| <div id="Analysis-Signal Analysis"> | | <div id="Analysis-Signal Analysis"> |
| <!-- Classic Heading --> | | <!-- Classic Heading --> |
− | <div id="Analysis-Background" class="col-md-12" style="padding:0"> | + | <div class="col-md-12" style="padding:0"> |
| <h3 class="classic-title" style="margin-top:50px"><span>Background</span></h3> | | <h3 class="classic-title" style="margin-top:50px"><span>Background</span></h3> |
| <!-- Some Text --> | | <!-- Some Text --> |
Line 192: |
Line 198: |
| <ol style="color:#606060;margin-top:0;margin-bottom:0;"> | | <ol style="color:#606060;margin-top:0;margin-bottom:0;"> |
| <li>There is no recognition site for gRNA in the mismatched gene.</li> | | <li>There is no recognition site for gRNA in the mismatched gene.</li> |
− | <li>The measure values <img alt='Peking-Analysis-X_iY_i.gif' src="https://static.igem.org/mediawiki/2015/c/cf/Peking-Analysis-X_iY_i.gif" class='formula-inline' style="width:120px"> | + | <li id="Analysis-Model">The measure values <img alt='Peking-Analysis-X_iY_i.gif' src="https://static.igem.org/mediawiki/2015/c/cf/Peking-Analysis-X_iY_i.gif" class='formula-inline' style="width:120px"> |
| of control and experimental group is independent of each other.</li> | | of control and experimental group is independent of each other.</li> |
| <li>The measure values from n times repeated test compose the <img alt='Peking-Analysis-X_iY_i.gif' src="https://static.igem.org/mediawiki/2015/c/cf/Peking-Analysis-X_iY_i.gif" class='formula-inline' style="width:120px"> sample set, respectively, and the sample sets are both small.</li> | | <li>The measure values from n times repeated test compose the <img alt='Peking-Analysis-X_iY_i.gif' src="https://static.igem.org/mediawiki/2015/c/cf/Peking-Analysis-X_iY_i.gif" class='formula-inline' style="width:120px"> sample set, respectively, and the sample sets are both small.</li> |
Line 199: |
Line 205: |
| <!--Analysis-Model--> | | <!--Analysis-Model--> |
| <!-- Classic Heading --> | | <!-- Classic Heading --> |
− | <div id="Analysis-Model" class="col-md-12" style="padding:0"> | + | <div class="col-md-12" style="padding:0"> |
| <h3 class="classic-title" style="margin-top:50px"><span>Model</span></h3> | | <h3 class="classic-title" style="margin-top:50px"><span>Model</span></h3> |
| <p><large><b>Wilcoxon Rank Sum Test of Block Design</b></large></p> | | <p><large><b>Wilcoxon Rank Sum Test of Block Design</b></large></p> |
Line 206: |
Line 212: |
| In the Block Design, we regarded the same gRNA detection of two treatment, i.e. target and mismatch DNA, as a block. To test the difference between two treatments, we test the null hypothesis that two treatment have no difference. The Wilcoxon Rank Sum statistics <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="width:30px">of each block is calculated first by | | In the Block Design, we regarded the same gRNA detection of two treatment, i.e. target and mismatch DNA, as a block. To test the difference between two treatments, we test the null hypothesis that two treatment have no difference. The Wilcoxon Rank Sum statistics <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="width:30px">of each block is calculated first by |
| <div align="center" class='row'> | | <div align="center" class='row'> |
− | <div class="col-md-2"></div>
| + | |
− | <img class='formula-line col-md-3' alt="Peking-Analysis-Wj%3DsumR_i" src="https://static.igem.org/mediawiki/2015/0/0e/Peking-Analysis-Wj%3DsumR_i.gif" style="max-width:400px"> | + | <img class='formula-line' alt="Peking-Analysis-Wj%3DsumR_i" src="https://static.igem.org/mediawiki/2015/3/34/Peking-Analysis-Wj%3DsumR_i_with_range.gif" style="max-height:60px"> |
− | <img class='formula-line col-md-5' alt="Peking-Analysis-W_j_range" src="https://static.igem.org/mediawiki/2015/5/5a/Peking-Analysis-W_j_range.gif" style="max-width:400px">
| + | |
− | <div class="col-md-3"></div>
| + | |
| </div></p> | | </div></p> |
| | | |
Line 236: |
Line 241: |
| <p>So the Wilcoxon Rank Sum Test may face challenge in single block test when the experimental and control group are slightly different.However, by using Block Design, we can integrate data from m blocks similar to the idea of ANOVA. We calculated the sum of <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="height:30px"> as the statistics. | | <p>So the Wilcoxon Rank Sum Test may face challenge in single block test when the experimental and control group are slightly different.However, by using Block Design, we can integrate data from m blocks similar to the idea of ANOVA. We calculated the sum of <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="height:30px"> as the statistics. |
| <div align='center'> | | <div align='center'> |
− | <img class='formula-line' alt="Peking-Analysis-W_sumWj.gif" src="https://static.igem.org/mediawiki/2015/2/29/Peking-Analysis-W_sumWj.gif" style='margin-top:0px;padding:0px;height:50px'> | + | <img class='formula-line' alt="Peking-Analysis-W_sumWj.gif" src="https://static.igem.org/mediawiki/2015/2/29/Peking-Analysis-W_sumWj.gif" style='margin-top:0px;padding:0px;height:60px'> |
| </div> | | </div> |
| <p>The Wilcoxon Rank Sum <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="height:30px"> from m blocks are independent and identically distributed (i.i.d), according to the central limit theorem (CLT), as m approaches infinity, the random variable <img class='big-formula-inline' alt="Peking-Analysis-W_BD_statistics.gif" src="https://static.igem.org/mediawiki/2015/6/68/Peking-Analysis-W_BD_statistics.gif" style="height:80px"> converges in distribution to a standard normal distribution <i>N</i>(0,1)</p> | | <p>The Wilcoxon Rank Sum <img alt='Peking-Analysis-W_j.gif' src="https://static.igem.org/mediawiki/2015/1/15/Peking-Analysis-W_j.gif" class='formula-inline' style="height:30px"> from m blocks are independent and identically distributed (i.i.d), according to the central limit theorem (CLT), as m approaches infinity, the random variable <img class='big-formula-inline' alt="Peking-Analysis-W_BD_statistics.gif" src="https://static.igem.org/mediawiki/2015/6/68/Peking-Analysis-W_BD_statistics.gif" style="height:80px"> converges in distribution to a standard normal distribution <i>N</i>(0,1)</p> |
Line 242: |
Line 247: |
| <img class='big-formula-line' alt="Peking-Analysis-W_BD_statistics_CLT.gif" src="https://static.igem.org/mediawiki/2015/7/73/Peking-Analysis-W_BD_statistics_CLT.gif "style="height:80px" style='margin:10px'> | | <img class='big-formula-line' alt="Peking-Analysis-W_BD_statistics_CLT.gif" src="https://static.igem.org/mediawiki/2015/7/73/Peking-Analysis-W_BD_statistics_CLT.gif "style="height:80px" style='margin:10px'> |
| </div> | | </div> |
− | <p>So actually we use the statistics <img class='big-formula-inline' alt="Peking-Analysis-W_BD_statistics.gif" src="https://static.igem.org/mediawiki/2015/6/68/Peking-Analysis-W_BD_statistics.gif" style="height:80px">, also we can calculate the p-value <img class='formula-inline' alt="Peking-Analysis-W_BD_p_value.gif" src="https://static.igem.org/mediawiki/2015/d/da/Peking-Analysis-W_BD_p_value.gif" style="height:30px">, where <img class='formula-inline' alt="Peking-Analysis-Phi%28x%29.gif" src="https://static.igem.org/mediawiki/2015/1/19/Peking-Analysis-Phi%28x%29.gif" style="height:30px"> is the distribution function of the standard normal distribution. If p-value is less than 0.01 or <img class='formula-inline' alt="Peking-Analysis-W_BD_gt_2.33.gif" src="https://static.igem.org/mediawiki/2015/2/20/Peking-Analysis-W_BD_gt_2.33.gif" style="height:30px">, then we accept the alternative hypothesis that the two treatment, i.e. target and mismatch DNA, is highly statistic significantly.</p> | + | <p>So actually we use the statistics <img class='big-formula-inline' alt="Peking-Analysis-W_BD_statistics.gif" src="https://static.igem.org/mediawiki/2015/6/68/Peking-Analysis-W_BD_statistics.gif" style="height:80px">, also we can calculate the p-value <img class='formula-inline' alt="Peking-Analysis-W_BD_p_value.gif" src="https://static.igem.org/mediawiki/2015/d/da/Peking-Analysis-W_BD_p_value.gif" style="height:35px">, where <img class='formula-inline' alt="Peking-Analysis-Phi%28x%29.gif" src="https://static.igem.org/mediawiki/2015/1/19/Peking-Analysis-Phi%28x%29.gif" style="height:30px"> is the distribution function of the standard normal distribution. If p-value is less than 0.01 or <img class='formula-inline' alt="Peking-Analysis-W_BD_gt_2.33.gif" src="https://static.igem.org/mediawiki/2015/2/20/Peking-Analysis-W_BD_gt_2.33.gif" style="height:30px">, <span id="Analysis-Result">then we</span> accept the alternative hypothesis that the two treatment, i.e. target and mismatch DNA, is highly statistic significantly.</p> |
| </div> | | </div> |
| </div> | | </div> |
| <!--End of Analysis-Model--> | | <!--End of Analysis-Model--> |
| <!--Start Result--> | | <!--Start Result--> |
− | <div id="Analysis-Result" class="col-md-12" style="padding:0"> | + | <div class="col-md-12" style="padding:0"> |
| <h3 class="classic-title" style="margin-top:50px"><span>Result</span></h3> | | <h3 class="classic-title" style="margin-top:50px"><span>Result</span></h3> |
| <div> | | <div> |
Line 254: |
Line 259: |
| </div> | | </div> |
| <div> | | <div> |
− | <p>In our experiment, <img alt='Peking-Analysis-n%3D3.gif' src="https://static.igem.org/mediawiki/2015/4/48/Peking-Analysis-n%3D3.gif" class='small-formula-inline'>, so | + | <p>In our experiment, <img alt='Peking-Analysis-n%3D3.gif' src="https://static.igem.org/mediawiki/2015/4/48/Peking-Analysis-n%3D3.gif" class='small-formula-inline' style="height:25px">, so |
− | <img alt='Peking-Analysis-E%28W_j%29.gif' src="https://static.igem.org/mediawiki/2015/a/a5/Peking-Analysis-E%28W_j%29.gif" class='formula-inline'> | + | <img alt='Peking-Analysis-E%28W_j%29.gif' src="https://static.igem.org/mediawiki/2015/a/a5/Peking-Analysis-E%28W_j%29.gif" class='formula-inline' style="height:40px;"> |
− | <img alt='Peking-Analysis-Var%28W_j%29.gif' src="https://static.igem.org/mediawiki/2015/a/ae/Peking-Analysis-Var%28W_j%29.gif" class='formula-inline'> | + | <img alt='Peking-Analysis-Var%28W_j%29.gif' src="https://static.igem.org/mediawiki/2015/a/ae/Peking-Analysis-Var%28W_j%29.gif" class='formula-inline' style="height:40px;"></p> |
| <div align='center'> | | <div align='center'> |
− | <img class='big-formula-line' alt="Peking-Analysis-W_BD_statistics_p_value.gif" src="https://static.igem.org/mediawiki/2015/1/1f/Peking-Analysis-W_BD_statistics_p_value.gif"></div> | + | <img class='big-formula-line' alt="Peking-Analysis-W_BD_statistics_p_value.gif" src="https://static.igem.org/mediawiki/2015/1/1f/Peking-Analysis-W_BD_statistics_p_value.gif" style="height:80px"></div> |
− | so target and mismatch DNA, are highly significantly different in signal.</p> | + | <p>so target and mismatch DNA, are highly significantly different in signal.</p> |
| </div> | | </div> |
| </div><!-- End Result--> | | </div><!-- End Result--> |
Line 276: |
Line 281: |
| | | |
| <!-- Start Subscribe & Social Links Widget --> | | <!-- Start Subscribe & Social Links Widget --> |
− | <div class="col-md-3">
| + | <div class="col-md-3"> |
| <div class="col-md-12 footer-widget social-widget row" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"> | | <div class="col-md-12 footer-widget social-widget row" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"> |
| <h4>Share This<span class="head-line"></span></h4> | | <h4>Share This<span class="head-line"></span></h4> |
| <ul class="social-icons" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"> | | <ul class="social-icons" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"> |
| <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> | | <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> |
− | <a class="twitter" target="_blank" href="https://twitter.com/home/?status=https://2015.igem.org/Team:Peking/Practices/Background"> | + | <a class="twitter" target="_blank" href="https://twitter.com/home/?status=https://2015.igem.org/Team:Peking"> |
| <i class="fa"> | | <i class="fa"> |
| <img src="https://static.igem.org/mediawiki/2015/d/d0/Peking-twitter.png" style="height:20px;width:auto; margin-top:7px;"> | | <img src="https://static.igem.org/mediawiki/2015/d/d0/Peking-twitter.png" style="height:20px;width:auto; margin-top:7px;"> |
Line 288: |
Line 293: |
| </li> | | </li> |
| <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> | | <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> |
− | <a class="facebook"target="_blank" href="https://www.facebook.com/sharer/sharer.php?u=https://2015.igem.org/Team:Peking/Practices/Background"> | + | <a class="facebook"target="_blank" href="https://www.facebook.com/sharer/sharer.php?u=https://2015.igem.org/Team:Peking"> |
| <i class="fa"> | | <i class="fa"> |
| <img src="https://static.igem.org/mediawiki/2015/0/0e/Peking-facebook.png" style="height:20px; margin-top:7px;"> | | <img src="https://static.igem.org/mediawiki/2015/0/0e/Peking-facebook.png" style="height:20px; margin-top:7px;"> |
Line 295: |
Line 300: |
| </li> | | </li> |
| <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> | | <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed--> |
− | <a class="google"target="_blank" href="https://plus.google.com/share?url=https://2015.igem.org/Team:Peking/Practices/Background"> | + | <a class="google"target="_blank" href="https://plus.google.com/share?url=https://2015.igem.org/Team:Peking"> |
| <i class="fa"> | | <i class="fa"> |
| <img src="https://static.igem.org/mediawiki/2015/7/7a/Peking-google_plus.png" style="height:20px; margin-top:7px;"> | | <img src="https://static.igem.org/mediawiki/2015/7/7a/Peking-google_plus.png" style="height:20px; margin-top:7px;"> |