YDPM-Yeast Deletion Project and Mitochondrial Proteomics Database

<table width="95%" border="0" cellspacing="0" cellpadding="4"> <tr bgcolor="#CCCC99" valign="middle"> <td width="21%"></td> <td width="79%"> <div align="center"> <p>Your browser does not support frames or you have frames turned off in your browser. You are viewing the "noframe" version of this web site. If you have problems with this web site please send mail to web.trebo@stanford.edu </p> <p><br> </p> </div> <h2 align="center"><font face="Verdana, Arial, Helvetica, sans-serif" color="#333300">Yeast Deletion Project and Mitochondrial Proteomics Database </font><font face="Verdana, Arial, Helvetica, sans-serif" color="#333300">Database<br> </font></h2> </td> </tr> <tr> <td width="21%"> </td> <td width="79%"> </td> </tr> <tr> <td height="116" width="21%"> <form name="ORF" method="get" action="/cgi-bin/YDPM/YDPM_search.cgi"> <h5> <textarea name="thelist" cols="10" rows="2"></textarea> <input type="submit" name="ORF" value="ORF"> </h5> </form> <form name="Gene" method="get" action="/cgi-bin/YDPM/YDPM_gene_search.cgi"> <h5> <textarea name="thelist" cols="10" rows="2"></textarea> <input type="submit" name="Gene" value="Gene"> </h5> </form> <hr size="2" width="98%"> <a href="/YDPM/doc/supplemental_data.html" class="extra"><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>Supplementary information for manuscript</b></font></a><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b> </b></font> <hr size="2" width="98%"> <b><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><a href="/YDPM/doc/guide.html">Guide to database entries and calculations</a></font></b> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>Analysis</b></font><font face="Verdana, Arial, Helvetica, sans-serif"><br> </font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="/YDPM/doc/class_I_candidates.part1.html">class I part 1<br> </a><a href="/YDPM/doc/class_I_candidates.part2.html">class I part 2</a><br> <a href="/YDPM/doc/class_I_candidates.part3.html">class I part 3</a><br> <a href="/YDPM/doc/class_I_candidates.part4.html">class I part 4</a><br> <a href="/YDPM/doc/class_II_candidates.html">class II</a><font size="1"><br> <a href="/YDPM/doc/class_IIIa_candidates.html">class IIIa</a><br> <a href="/YDPM/doc/class_IIIb_candidates.html">class IIIb</a></font><br> <a href="/YDPM/doc/class_III_final_cand_466.html">- 466 final candidates</a><br> <a href="/YDPM/doc/class_III_final_cand_161unknown.html">- 161 unclassified ORFs</a><font size="1"><br> </font></font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="/YDPM/doc/class_III_final_cand_201mitoch.html">- 201 mitochondrial proteins</a><font size="1"><br> <a href="/YDPM/doc/class_III_final_cand_104nonmit.html">- 104 non-mito. proteins</a></font></font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><br> </font></p> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>Download Data<br> </b></font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="http://www-deletion.stanford.edu/YDPM/Regression_Tc1_hom.txt" >Regression_Tc1_hom.txt</a></font><br> <font size="1" face="Verdana, Arial, Helvetica, sans-serif"><a href="http://www-deletion.stanford.edu/YDPM/Regression_Tc2_hom.txt" >Regression_Tc2_hom.txt</a></font><br> <font size="1" face="Verdana, Arial, Helvetica, sans-serif"><a href="http://www-deletion.stanford.edu/YDPM/Regression_Tc1_het.txt" >Regression_Tc1_het.txt</a></font><br> <font size="1" face="Verdana, Arial, Helvetica, sans-serif"><a href="http://www-deletion.stanford.edu/YDPM/Regression_Tc2_het.txt" >Regression_Tc2_het.txt</a></font> </p> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>Homology</b></font><font face="Verdana, Arial, Helvetica, sans-serif"><br> <font size="1"><a href="/YDPM/doc/homology_R_prowazekii.html">R.prowazekii</a><br> <a href="/YDPM/doc/homol_bact_prot.html">Bacterial proteins</a></font></font></p> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>Prediction</b></font><font face="Verdana, Arial, Helvetica, sans-serif"><br> </font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="/YDPM/doc/MitoP.html">MitoP</a><br> <a href="/YDPM/doc/Mitoprot.html">Mitoprot</a></font></p> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2"><b>External data</b></font><font face="Verdana, Arial, Helvetica, sans-serif"><br> </font><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="/YDPM/doc/slow_growth.html">slow growth</a><br> <a href="/YDPM/doc/respiratory_deficient.html">respiratory deficient</a><br> <a href="/YDPM/doc/carbohydrate_utiliz_defect.html">carbohydrate utilization defect</a><br> <a href="/YDPM/doc/carbohydrate_metabolism.html">carbohydrate metabolism</a></font><font size="1" face="Verdana, Arial, Helvetica, sans-serif"><br> <a href="/YDPM/doc/regulators_carbohydrate_metab.html">regulators of carb. metabolism</a> </font></p> <p> </p> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="1"><a href="mailto:curts@stanford.edu,larsms@leland.stanford.edu">Contact Authors</a></font> </p> </td> <td width="79%"> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">In this project strains from the <a class="extra" href="http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html"><b>yeast deletion project</b></a> were monitored under 9 different media conditions using molecular barcodes. This database contains both the raw data and growth rates calculated for each strain in each media condition. Strains can be searched by ORF name or gene name to access plots and growth measures for each strain. The database is hyperlinked with public databases of other yeast resources (<a href = "http://www.yeastgenome.org/Saccharomyces/"><b>SGD</b></a>, <a href = "http://www.proteome.com/databases/YPD/YPDsearch-quick.html"><b>YPD</b></a>, <a href = "http://mips.gsf.de/proj/yeast/CYGD/db/index.html"><b>CYGD</b></a>, <a href = "http://mips.gsf.de/cgi-bin/proj/medgen/homeyeast"><b>MITOP</b></a>). </font></p> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">5791 heterozygous diploid and 4706 homozygous diploid deletion strains were monitored in parallel on fermentable (YPD, YPDGE) and non-fermentable substrates (YPG, YPE, YPL). The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. </font></p> <hr width="45%" align="center"> <h5 align="left"><font face="Verdana, Arial, Helvetica, sans-serif"><font color="#000000"><b>Specific Information on the links:</b></font></font></h5> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">Under <b>Analysis</b>, the homozygous diploid strains were grouped into three classes: class I lists genes without significant growth differences between conditions; class II has genes with a fermentable growth defect; class III genes with a non-fermentable growth deficiency. Each list is interlinked with the database. In an additional analysis class IIIa and class IIIb were combined (different degrees of non-fermentable growth defects) and narrowed to 466 genes by removing spurious ORFs. The 466 genes were divided into 201 previously known mitochondrial genes (localization or function); 161 with unknown localization; 104 localized outside mitochondria.</font></p> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">Under <b>Homology</b> yeast genes are listed that are similar to proteins in Rickettsia prowazeckii and bacteria in general.</font></p> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">Under <b>Prediction</b> yeast genes are listed according to whether they are known mitochondria-related proteins (MitoP) or have a high probability of containing a mitochondrial import sequence (Mitoprot).</font></p> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">Under <b>External data</b> are functional and phenotypic classifications acquired from public databases, mostly from CYGD.</font></p> <p align="left"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">All data are available for <b>download</b> from homozygous and heterozygous pools (two repeat experiments).</font></p> <hr width="45%" align="center"> <h5 align="left"><font face="Verdana, Arial, Helvetica, sans-serif"><b><font color="#000000">This database serves to support:</font></b></font></h5> <p><font face="Verdana, Arial, Helvetica, sans-serif" size="2">Lars M. Steinmetz, Curt Scharfe, Adam M. Deutschbauer, Dejana Mokranjac, Zelek S. Herman, Ted Jones, Angela Chu, Guri Giaever, Holger Prokisch, Peter J. Oefner & Ronald Davis. <b><a href="/YDPM/doc/supplemental_data.html" class="extra">Systematic screen for human disease genes in yeast</a></b>. Submitted. </font></p> <hr> <p align="center"><font size="-1">Web site © 2002 Stanford Genome Technology Center</font></p> <p align="center"><font size="-1"> In addition to original data, this web site and its associated links contain information gleened from public data. While the public data has been faithfully downloaded into the YDPM database, no representations are made regarding the accuracy of the public data.</font></p> <p align="center"><font size="-1"> <a href="mailto:herman@sequence.stanford.edu">Web site administrator</a></font></p> </td> </tr> </table>