OSF | Reproducibility Project: Cancer Biology Wiki

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19:09:40+00:00 UTC</option> <option value="13">(13) Tim Errington: 2013-10-24 19:08:03+00:00 UTC</option> <option value="12">(12) Tim Errington: 2013-10-23 20:33:04+00:00 UTC</option> <option value="11">(11) Tim Errington: 2013-10-23 18:13:56+00:00 UTC</option> <option value="10">(10) Tim Errington: 2013-10-23 18:12:22+00:00 UTC</option> <option value="9">(9) Tim Errington: 2013-10-23 18:12:00+00:00 UTC</option> <option value="8">(8) Tim Errington: 2013-10-23 18:05:57+00:00 UTC</option> <option value="7">(7) Tim Errington: 2013-10-23 18:00:48+00:00 UTC</option> <option value="6">(6) Tim Errington: 2013-10-23 18:00:23+00:00 UTC</option> <option value="5">(5) Tim Errington: 2013-10-23 17:59:54+00:00 UTC</option> <option value="4">(4) Tim Errington: 2013-10-23 17:52:45+00:00 UTC</option> <option value="3">(3) Tim Errington: 2013-10-23 17:50:38+00:00 UTC</option> <option value="2">(2) Tim Errington: 2013-10-23 17:48:36+00:00 UTC</option> <option value="1">(1) Tim Errington: 2013-10-23 17:48:24+00:00 UTC</option> </select> </div> </div> </div> </div> </div> <div id="wikiViewPanel" class="panel-body" data-bind="css: { 'osf-panel-body-flex': $root.singleVis() !== 'view' }"> <div id="wikiViewRender" data-bind="html: renderedView, mathjaxify: renderedView, anchorScroll : { buffer: 50, elem : '#wikiViewPanel'}" class="markdown-it-view scripted"> <h2>The Reproducibility Project: Cancer Biology is a collaboration between <a href="https://www.scienceexchange.com" rel="nofollow">Science Exchange</a> and the <a href="https://cos.io" rel="nofollow">Center for Open Science</a>, and is independently replicating a subset of experimental results from a number of high-profile papers in the field of cancer biology published between 2010-2012 using the Science Exchange network of expert scientific labs.</h2> <hr> <h3>Replication Study Results</h3> <p><br></p> <p>All published articles related to the project can be found on the <a href="http://elifesciences.org/collections/reproducibility-project-cancer-biology" rel="nofollow">Reproducibility Project: Cancer Biology collection</a> at <a href="https://elifesciences.org" rel="nofollow"><em>eLife</em></a>. Each replication is being organized on the <a href="https://osf.io" rel="nofollow">Open Science Framework</a> (OSF). The OSF is a free service and is where all the experimental protocols, materials, data, analysis, and results will made openly available to the public. Furthermore, quality assurance will be maintained with the <a href="https://osf.io/8mpji/wiki/home/" rel="nofollow">Registered Reports</a> format, in which peer review of proposed experimental designs and protocols will be conducted prior to data collection, in conjunction with <em>eLife</em> with the eventual results published in a Replication Study. <br></p> <p>At this time, sixteen Replication Studies have been published: <br></p> <p><strong>Replication Study: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/51019" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/yyqas/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/08245" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> <li>View the <a href="https://elifesciences.org/articles/56397" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/45120" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/7yqmp/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/04796" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> <li>View the <a href="https://elifesciences.org/articles/53511" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: Wnt activity defines colon cancer stem cells and is regulated by the microenvironment</strong></p> <ul> <li>View the <a href="https://doi.org/10.7554/eLife.45426" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/pgjhx/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/07301" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: The microRNA miR-34a inhibits prostate cancer stem cells and metastasis by directly repressing CD44</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/43511" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/gb7sr/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/06434" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/39944" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/ewqzf/wiki/home" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/07383" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/34364" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/y4tvd/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/04186" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: <em>Fusobacterium nucleatum</em> infection is prevalent in human colorectal carcinoma</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/25801" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/v4se2/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/10012" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> <li>View the <a href="https://elifesciences.org/articles/28434" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc</strong></p> <ul> <li>View the <a href="https://doi.org/10.7554/eLife.30274" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/mokeb/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/04024" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> <li>View the <a href="https://elifesciences.org/articles/32010" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: Systematic identification of genomic markers of drug sensitivity in cancer cells</strong></p> <ul> <li>View the <a href="https://doi.org/10.7554/eLife.29747" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/nbryi/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/13620" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/25306" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/hcqqy/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/08997" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate</strong></p> <ul> <li>View the <a href="https://elifesciences.org/articles/26030" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/8l4ea/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/articles/12626v1" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: Coadministration of a Tumor-Penetrating Peptide Enhances the Efficacy of Cancer Drugs</strong></p> <ul> <li>View the <a href="http://dx.doi.org/10.7554/eLife.17584" rel="nofollow">Replication Study results</a> published in <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/xu1g2/wiki/home/" rel="nofollow">OSF Project page</a> to view all data, methods, and materials pertaining to this Replication Study.</li> <li>View the <a href="https://elifesciences.org/content/4/e06959" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this Replication Study.</li> </ul> <p><strong>Replication Study: BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc</strong></p> <ul> <li>View the <a href="http://dx.doi.org/10.7554/eLife.21253" rel="nofollow">Replication Study results</a> published in <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/7zqxp/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/content/4/e07072" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this Replication Study.</li> <li>View the <a href="http://dx.doi.org/10.7554/eLife.22915" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: Discovery and Preclinical Validation of Drug Indications using Compendia of Public Gene Expression Data</strong></p> <ul> <li>View the <a href="http://dx.doi.org/10.7554/eLife.17044" rel="nofollow">Replication Study results</a> published in <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/hxrmm/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/content/4/e06847" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this Replication Study.</li> <li>View the <a href="http://dx.doi.org/10.7554/eLife.22661" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <p><strong>Replication Study: The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors</strong></p> <ul> <li>View the <a href="http://dx.doi.org/10.7554/eLife.18173" rel="nofollow">Replication Study results</a> published in <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/9pbos/wiki/home/" rel="nofollow">OSF Project page</a>, which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/content/4/e04586" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> </ul> <p><strong>Replication Study: Melanoma genome sequencing reveals frequent PREX2 mutations</strong></p> <ul> <li>View the <a href="http://dx.doi.org/10.7554/eLife.21634" rel="nofollow">Replication Study results</a> published by <em>eLife</em>.</li> <li>Access the <a href="https://osf.io/jvpnw/wiki/home/" rel="nofollow">OSF Project page</a> which contains all data, methods, and materials pertaining to the replication of this Replication Study.</li> <li>View the <a href="https://elifesciences.org/content/3/e04180" rel="nofollow">Registered Report</a>, which contains detailed, peer-reviewed, protocols for this replication.</li> <li>View the <a href="http://dx.doi.org/10.7554/eLife.22662" rel="nofollow">Insight article</a> published alongside this Replication Study.</li> </ul> <hr> <h3>Additional articles and commentary published on this project:</h3> <p>For more information read the <a href="https://elifesciences.org/content/3/e04333" rel="nofollow">Introductory commentary</a> published by <em>eLife</em> that introduces and summarizes the project and the corresponding <a href="https://elifesciences.org/content/3/e03981" rel="nofollow">editorial</a> as well as the <a href="http://dx.doi.org/10.7554/eLife.23383" rel="nofollow">Replication commentary</a> and the corresponding <a href="http://dx.doi.org/10.7554/eLife.23693" rel="nofollow">editorial</a> from <em>eLife</em>.</p> <hr> <h3>Interested in helping assess reproducibility?</h3> <p>What is a successful replication? This seemingly simple question is not sufficiently described by any single indicator. Because success in replication is complex, the RP:CB aims to assess replication using multiple approaches. One of these is subjective assessment. We are seeking to recruit scientists in biomedical research to review the results of the replications and give their subjective opinion of whether the original result was successfully replicated. Currently we are collecting a list of interested scientists. A formal survey will be available before the replication results are made public. We will reach out to scientists on our list at that time to take the survey. The project is still ongoing, so it might be a few weeks, months, or sometime next year when a survey becomes available. If interested, view the <a href="http://elifesciences.org/collections/reproducibility-project-cancer-biology" rel="nofollow">active replications</a> and go to the <a href="https://docs.google.com/forms/d/e/1FAIpQLSev7dmgbYjprYrAPD5y7nUo4raI__06VR_3E5nf_6m4XUxUOQ/viewform" rel="nofollow">registration page</a> to register for the subjective assessment.</p> <hr> <h3>What are the aims of the project?</h3> <p>Through independent direct replication studies, the project aims to identify best practices that maximize reproducibility and facilitate an accurate accumulation of knowledge, enabling potentially impactful novel findings to be effectively built upon by the scientific community. </p> <p>Additionally we expect to learn about:</p> <ul> <li>The overall rate of reproducibility in a sample of the published cancer biology literature.</li> <li>Obstacles that arise in conducting direct replications of original studies.</li> <li>The feasibility and practical challenges of getting proper materials, methods, and instrumentation for a replication.</li> <li>Predictors of replication success such as the journal in which the original finding was published, the citation impact of the original report, the number of direct replications that have been published elsewhere, the transparency of materials and methods included with the publication, and adherence to publishing checklists and guidelines.</li> </ul> <hr> <h3>Additional Information</h3> <p>The Reproducibility Project: Cancer Biology is managed by a core team of personnel who develops and executes the project design. A standardized procedure is followed to minimize irrelevant variation between each replication and to maximize the quality of the replication efforts. An summary of the project process is available <a href="https://docs.google.com/document/d/1TE2vKQ8h-5Fxk7NFIVBxdog5DckVGj3Ipw_gLRJsrZ8/edit" rel="nofollow">here</a>. A biography of each of the core team members can be viewed on the <a href="https://osf.io/e81xl/wiki/Core%20Project%20Team/" rel="nofollow">Core Project Team</a> page. Funding and supporting organization for this project can be seen by visiting the <a href="https://osf.io/e81xl/wiki/Funding%20and%20Supporting%20Organizations/" rel="nofollow">Funding and Supporting Organizations</a> page. For additional information please visit the <a href="https://osf.io/e81xl/wiki/Press/" rel="nofollow">Press</a> and <a href="https://osf.io/e81xl/wiki/Frequently%20Asked%20Questions%20%28FAQ%29/" rel="nofollow">FAQ</a> pages.</p> <p>Questions or are interest in supporting the project can be directed to <a href="mailto:contact+rpcb@cos.io">contact+rpcb@cos.io</a>.</p> <hr> </div> </div> </div> </div> <div data-osf-panel="Compare" class="col-sm-12.0" style="display: none"> <div class="osf-panel panel panel-default osf-panel-flex" data-bind="css: { 'no-border reset-height': $root.singleVis() === 'compare', 'osf-panel-flex': $root.singleVis() !== 'compare' }"> <div class="panel-heading osf-panel-heading-flex" data-bind="css: { 'osf-panel-heading-flex': $root.singleVis() !== 'compare', 'wiki-single-heading': $root.singleVis() === 'compare'}"> <div class="row"> <div class="col-xs-12"> <span class="panel-title m-r-xs"> <i class="fa fa-exchange"> </i> Compare </span> <div class="inline" data-bind="css: { 'pull-right' : $root.singleVis() === 'compare' }">  <span class="compare-version-text"><i> <span data-bind="text: viewVersionDisplay"></span></i> to <select class="form-control" data-bind="value: compareVersion" id="compareVersionSelect"> <option value="current">(Current) Tim Errington: 2020-04-21 19:38:18+00:00 UTC</option> <option value="111">(111) Tim Errington: 2020-04-21 19:36:12+00:00 UTC</option> <option value="110">(110) Tim Errington: 2019-12-17 14:58:10+00:00 UTC</option> <option value="109">(109) Tim Errington: 2019-12-17 14:56:40+00:00 UTC</option> <option value="108">(108) Tim Errington: 2019-12-17 14:49:36+00:00 UTC</option> <option value="107">(107) Tim Errington: 2019-06-19 14:31:48+00:00 UTC</option> <option value="106">(106) Tim Errington: 2019-06-19 14:30:20+00:00 UTC</option> <option value="105">(105) Tim Errington: 2019-04-02 12:29:41+00:00 UTC</option> <option value="104">(104) Tim Errington: 2019-04-02 12:28:59+00:00 UTC</option> <option 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15:01:38+00:00 UTC</option> <option value="39">(39) Tim Errington: 2014-01-13 17:18:39+00:00 UTC</option> <option value="38">(38) Tim Errington: 2014-01-13 17:16:39+00:00 UTC</option> <option value="37">(37) Tim Errington: 2014-01-13 17:15:38+00:00 UTC</option> <option value="36">(36) Tim Errington: 2014-01-13 17:15:07+00:00 UTC</option> <option value="35">(35) Tim Errington: 2014-01-13 16:39:47+00:00 UTC</option> <option value="34">(34) Tim Errington: 2014-01-13 16:19:08+00:00 UTC</option> <option value="33">(33) Tim Errington: 2014-01-13 16:18:01+00:00 UTC</option> <option value="32">(32) Tim Errington: 2014-01-13 16:17:35+00:00 UTC</option> <option value="31">(31) Tim Errington: 2014-01-13 16:09:14+00:00 UTC</option> <option value="30">(30) Tim Errington: 2013-11-05 21:10:31+00:00 UTC</option> <option value="29">(29) Tim Errington: 2013-10-24 23:49:01+00:00 UTC</option> <option value="28">(28) Tim Errington: 2013-10-24 23:45:38+00:00 UTC</option> <option value="27">(27) Tim Errington: 2013-10-24 23:40:50+00:00 UTC</option> <option value="26">(26) Tim Errington: 2013-10-24 23:40:34+00:00 UTC</option> <option value="25">(25) Tim Errington: 2013-10-24 23:40:22+00:00 UTC</option> <option value="24">(24) Tim Errington: 2013-10-24 23:39:47+00:00 UTC</option> <option value="23">(23) Tim Errington: 2013-10-24 20:06:21+00:00 UTC</option> <option value="22">(22) Tim Errington: 2013-10-24 19:50:10+00:00 UTC</option> <option value="21">(21) Tim Errington: 2013-10-24 19:49:12+00:00 UTC</option> <option value="20">(20) Tim Errington: 2013-10-24 19:38:43+00:00 UTC</option> <option value="19">(19) Tim Errington: 2013-10-24 19:37:29+00:00 UTC</option> <option value="18">(18) Tim Errington: 2013-10-24 19:20:29+00:00 UTC</option> <option value="17">(17) Tim Errington: 2013-10-24 19:17:59+00:00 UTC</option> <option value="16">(16) Tim Errington: 2013-10-24 19:14:11+00:00 UTC</option> <option value="15">(15) Tim Errington: 2013-10-24 19:10:48+00:00 UTC</option> <option value="14">(14) Tim Errington: 2013-10-24 19:09:40+00:00 UTC</option> <option value="13">(13) Tim Errington: 2013-10-24 19:08:03+00:00 UTC</option> <option value="12">(12) Tim Errington: 2013-10-23 20:33:04+00:00 UTC</option> <option value="11">(11) Tim Errington: 2013-10-23 18:13:56+00:00 UTC</option> <option value="10">(10) Tim Errington: 2013-10-23 18:12:22+00:00 UTC</option> <option value="9">(9) Tim Errington: 2013-10-23 18:12:00+00:00 UTC</option> <option value="8">(8) Tim Errington: 2013-10-23 18:05:57+00:00 UTC</option> <option value="7">(7) Tim Errington: 2013-10-23 18:00:48+00:00 UTC</option> <option value="6">(6) Tim Errington: 2013-10-23 18:00:23+00:00 UTC</option> <option value="5">(5) Tim Errington: 2013-10-23 17:59:54+00:00 UTC</option> <option value="4">(4) Tim Errington: 2013-10-23 17:52:45+00:00 UTC</option> <option value="3">(3) Tim Errington: 2013-10-23 17:50:38+00:00 UTC</option> <option value="2">(2) Tim Errington: 2013-10-23 17:48:36+00:00 UTC</option> <option 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