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105<div class='box_title'>STITCH Database &#8212; Content</div>
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107<div class='footer_text_page_boring'>STITCH is a database of known and predicted interactions between chemicals and proteins. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.<br/><h2>Data Sources</h2>Interactions in STITCH are derived from five main sources:<br/>&nbsp;<br/><table class='footer_content_table'><tr><td><img src='/images/genome_context.png'/><br/>Genomic Context Predictions</td><td><img src='/images/experiment_title.png'/><br/>High-throughput Lab Experiments</td><td><img src='/images/conserved_coexpression.png'/><br/>(Conserved) Co-Expression</td><td><img src='/images/textmining_content.png'/><br/>Automated Textmining</td><td><img src='/images/database_content.png'/><br/>Previous Knowledge in Databases</td></tr></table><h2>Coverage</h2>The STITCH database currently covers 9'643'763 proteins from 2'031 organisms.</div></div></div></div><div class='switching_form' id='sf_contributors' style='display:none'><div class='footer_display_box'>
108<div class='box_title'>STITCH Database &#8212; Contributors</div>
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110<div class='footer_text_page_boring'><table class='footer_contribution_table'><tr><td><h2>Swiss Institute of Bioinformatics</h2><a href='http://www.imls.uzh.ch/research/vonmering/people/damian-szklarczyk.html'>Damian Szklarczyk</a><br/><a href='http://www.imls.uzh.ch/research/vonmering/people/milan-simonovic.html'>Milan Simonovic</a><br/><a href='http://www.imls.uzh.ch/research/vonmering.html'>Christian von Mering</a><br/></td><td><h2>NNF Center for Protein Research</h2><a href='http://www.cpr.ku.dk/staff/385200/?pure=en/persons/500317'>Helen Victoria Cook</a><br/>

110<a href='http://www.cpr.ku.dk/staff/385200/?pure=en/persons/469855'>Alberto Santos Delgado</a><br/><a href='http://www.cpr.ku.dk/staff/staff_all/?pure=en/persons/343848'>Lars Juhl Jensen</a><br/></td></tr><tr><td><h2>EMBL Heidelberg</h2><a href='http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=CP-60014446'>Kristoffer Forslund</a><br/><a href='http://www.embl.de/research/units/scb/bork/members/?s_personId=CP-60003241'>Peer Bork</a><br/><a href='http://www.mckuhn.de/'>Michael Kuhn</a><br/></td></tr><tr><td colspan='2'><h2>University of Zurich</h2><a href='http://www.imls.uzh.ch/research/vonmering/people/alexander-roth.html'>Alexander Roth</a><br/><a href='http://www.imls.uzh.ch/research/vonmering.html'>Christian von Mering</a><br/></td></tr><tr><td colspan='2'><h2>Former Contributors</h2>Samuel Chaffron, Tobias Doerks, Mathilde Foglierini, Andrea Franceschini, Davide Heller, Sean Hooper, Martijn Huynen, Daniel Jaeggi, Nelly Jouffre, Beate Krueger, Markus Krupp, Gerrit Lehmann, Pablo Minguez, Jean Muller, Steffen Schmidt, Berend Snel, Stefan Wyder.</td></tr></table></div></div></div></div><div class='switching_form' id='sf_references' style='display:none'><div class='footer_display_box'>
111<div class='box_title'>STITCH Database &#8212; References</div>
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113<div class='footer_text_page_boring'>When using STITCH, please consult (and cite) any of the following references:</br>&nbsp;<br/>Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.<br>
114<strong><a href="http://www.ncbi.nlm.nih.gov/pubmed/26590256">STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.</a></strong><br>
115Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4.<br>
116<br>
117Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.<br>
118<strong><a href="http://www.ncbi.nlm.nih.gov/pubmed/24293645">STITCH 4: integration of protein-chemical interactions with user data.</a></strong><br>
119Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7.<br>
120<br>
121Kuhn M, Szklarczyk D*, Franceschini A, von Mering C, Jensen LJ, Bork P.<br>
122<strong><a href="http://www.ncbi.nlm.nih.gov/pubmed/22075997">STITCH 3: zooming in on protein-chemical interactions.</a></strong><br>
123Nucleic Acids Res. 2012 Jan;40(Database issue):D876-80.<br>
124<br>
125Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P.<br>
126<strong><a href="http://www.ncbi.nlm.nih.gov/pubmed/19897548">STITCH 2: an interaction network database for small molecules and proteins.</a></strong><br>
127Nucleic Acids Res. 2010 Jan;38(Database issue):D552-6.<br>
128<br>
129Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P.<br>
130<strong><a href="http://www.ncbi.nlm.nih.gov/pubmed/18084021">STITCH: interaction networks of chemicals and proteins.</a></strong><br>
131Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8.<br>
132</div></div></div></div><div class='switching_form' id='sf_statistics' style='display:none'><div class='footer_display_box'>
133<div class='box_title'>STITCH Database &#8212; Statistics</div>
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135<div class='footer_text_page_boring'><h2>Number of organisms</h2>
136<table class='footer_stats_table'><tr><td>1'678</td><td>&nbsp;Bacteria</td></tr><tr><td>238</td><td>&nbsp;Eukaryotes</td></tr><tr><td>115</td><td>&nbsp;Archaea</td></tr><tr class='sum_total'><td><span>2'031</span></td><td><span>&nbsp;total organisms</span></td></tr></table>
137<h2>Number of proteins</h2>
1389'643'763 proteins<h2>Number of interactions (by confidence level)</h2>
139<table class='footer_stats_table'><tr><td>26'217'572</td><td>&nbsp;interactions at highest confidence (score >= 0.900)</td></tr><tr><td>66'020'990</td><td>&nbsp;interactions at high confidence or better (score >= 0.700)</td></tr><tr><td>184'805'933</td><td>&nbsp;interactions at medium confidence or better (score >= 0.400)</td></tr><tr><td>931'727'375</td><td>&nbsp;interactions at low confidence or better (score >= 0.150)</td></tr><tr><td>826'522</td><td>&nbsp;interactions below low confidence (score < 0.150)</td></tr><tr class='sum_total'><td><span>932'553'897</span></td><td>

139<span>&nbsp;total interactions</span></td></tr></table>
140<h2>Top organisms (by query volume)</h2>
1411. Homo sapiens<br/>2. Mus musculus<br/>3. Escherichia coli<br/>4. Arabidopsis thaliana<br/>5. Caenorhabditis elegans<br/>6. Saccharomyces cerevisiae<br/>7. Rattus norvegicus<br/>8. Drosophila melanogaster<br/>9. Bacillus subtilis<br/>10. Pseudomonas aeruginosa PAO1<br/></div></div></div></div></div></div></div></div></div></div></div>

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