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+<META NAME="Generator" CONTENT="TextPad 4.6">\r
+<META NAME="Author" CONTENT="?">\r
+<META NAME="Keywords" CONTENT="?">\r
+<META NAME="Description" CONTENT="?">\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="#FFFFFF" TEXT="#000000" LINK="#3333FF" VLINK="#663399" ALINK="#FF00FF" BACKGROUND="#e5e5e5">\r
+<blockquote>\r
+\r
+<center><h1>Plant Metabolic Pathways</h1></center>\r
+<p></p>\r
+ <table align="center" border="0" cellpadding="2" cellspacing="2" height="360" width="90%">\r
+\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><b>RiceCyc</b> ver 3.3 <b><img alt="" src="http://archive.gramene.org/pathway/ricecyc.gif" align="right" height="40" width="84" /></b><i><br />\r
+Oryza sativa japonica</i> <br />\r
+Strain: Nipponbare<br /><a href="http://palea.cgrb.oregonstate.edu:1555/RICE/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/ricecyc.shtml">More info</a><br />\r
+</td>\r
+<td valign="top" width="32%"><b>AraCyc*</b> ver 10.0 <img alt="" src="http://archive.gramene.org/pathway/aracyc_logo.gif" align="right" height="38" width="65" /><br />\r
+<i>Arabidopsis thaliana</i> <br />\r
+Strain: Columbia<br /> <a href="http://palea.cgrb.oregonstate.edu:1555/ARA/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/ARA/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/aracyc.shtml">More info</a><br />\r
+</td>\r
+<td valign="top" width="35%"><b>EcoCyc*</b> ver 17.0 <img alt="" src="http://archive.gramene.org/pathway/EcoCyc.gif" align="right" height="40" width="125" /><br />\r
+<i>Escherichia coli</i> <br />\r
+Strain: K-12 MG1655<br /><a\r
+href="http://palea.cgrb.oregonstate.edu:1555/ECOLI/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/ECOLI/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/ecocyc.shtml">More info</a><br /><br />\r
+</td>\r
+</tr>\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><b>SorghumCyc</b> ver 1.1 <img alt="" src="http://archive.gramene.org/pathway/sorghumcyc.png" align="right" border="0" height="18" width="84" /> <br />\r
+<i>Sorghum bicolor</i> <br />\r
+Strain: BTx623<br /><a href="http://palea.cgrb.oregonstate.edu:1555/SORGHUM/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/SORGHUM/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/sorghumcyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="32%"><b>MedicCyc*</b> ver 1.0.1 <img alt="" src="http://archive.gramene.org/pathway/medicago.jpg" align="right" height="43" width="45" /><br />\r
+<i>Medicago truncatula</i>, Barrelclover<br />\r
+Unavailable<br /> <a href="http://palea.cgrb.oregonstate.edu:1555/MEDIC/class-tree?object=Pathways"-->Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/MEDIC/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/mediccyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="35%"><b>MetaCyc*</b> ver 17.0 <img alt="" src="http://archive.gramene.org/pathway/MetaCyc.gif" align="right" height="30" width="125" /><br />\r
+Reference Pathway Database<br />\r
+Strain: not applicable<br /><a\r
+href="http://palea.cgrb.oregonstate.edu:1555/META/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/META/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/metacyc.shtml">More info</a><br /><br />\r
+</td>\r
+</tr>\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><b>MaizeCyc</b> ver 2.1 <img alt="" src="http://archive.gramene.org/pathway/maizecyc.jpg" align="right" border="0" height="45" width="132" /> <br />\r
+<i>Zea mays</i> <br />\r
+Strain: B73<br /><a href="http://palea.cgrb.oregonstate.edu:1555/MAIZE/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/MAIZE/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/maizecyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="35%"><b>PoplarCyc*</b> ver 5.0 <img alt="" src="http://archive.gramene.org/pathway/poplarcyc_logo.gif" align="right" height="30" width="125" /><br />\r
+Populus trichocarpa (and other Populus species and hybrids)<br />\r
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/POPLAR/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/POPLAR/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/poplarcyc.shtml">More info</a><br /><br />\r
+</td>\r
+\r
+<td valign="top" width="35%"><b>PlantCyc*</b> ver 7.0 <img alt="" src="http://archive.gramene.org/pathway/plantcyc_logo.gif" align="right" height="30" width="125" /><br />\r
+Plant Metabolic Pathway Database<br />\r
+Strain: not applicable<br /><a href="http://palea.cgrb.oregonstate.edu:1555/PLANT/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/PLANT/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/plantcyc.shtml">More info</a><br /><br />\r
+</td>\r
+</tr>\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><b>BrachyCyc</b> ver 2.0 <img alt=""\r
+src="http://archive.gramene.org/pathway/brachycyc.jpg" align="right" border="0" height="45" width="132" /> <br /> <i>Brachypodium distachyon</i> <br />\r
+Strain: Bd21<br /><a href="http://palea.cgrb.oregonstate.edu:1555/BRACHY/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/BRACHY/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/brachycyc.shtml">More info</a><br /><br />\r
+</td>\r
+\r
+<!--td valign="top" width="32%"><b>CapCyc*</b> ver 1.0.1.1 <img alt="" src="http://archive.gramene.org/pathway/pepper.gif" align="right" height="26" width="45" /><br /-->\r
+<!--i>Capsicum anuum</i>, Pepper<br /-->\r
+<!--Strain: n/a<br /> <a href="/CAP/class-tree?object=Pathways">Browse</a> | <a href="/CAP/organism-summary?">Summary</a> | <a href="/gramene/capcyc.shtml">More info</a><br /><br /-->\r
+<!--/td-->\r
+\r
+<!--/tr-->\r
+<!--tr class="searchbody"-->\r
+<!--td valign="top" width="32%"><br /-->\r
+<!--/td-->\r
+<td valign="top" width="32%"><b>PotatoCyc*</b> ver 1.0.1 <img alt="" src="http://archive.gramene.org/pathway/potato.jpg" align="right" height="45" width="45" /><br />\r
+<i>Solanum tuberosum</i>, Potato<br />\r
+Strain: n/a <br /> <a href="http://palea.cgrb.oregonstate.edu:1555/POTATO/class-tree?object=Pathways"-->Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/POTATO/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/potatocyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="35%"><br />\r
+</td>\r
+</tr>\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><br />\r
+</td>\r
+<td valign="top" width="32%"><b>CoffeaCyc*</b> ver 1.1.1 <img alt="" src="http://archive.gramene.org/pathway/coffee.jpg" align="right" height="46" width="45" /><br />\r
+<i>Coffea canephora</i>, Coffee<br />\r
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/COFFEA/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/COFFEA/organism-summary?"-->Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/coffeacyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="35%"><br />\r
+</td>\r
+</tr>\r
+\r
+<tr class="searchbody">\r
+<td valign="top" width="32%"><br />\r
+</td>\r
+<td valign="top" width="32%"><b>LycoCyc*</b> ver 2.0.1 <img alt="" src="http://archive.gramene.org/pathway/tomato.jpg" align="right" height="45" width="45" /><br />\r
+<i>Solanum lycopersicum</i>, Tomato<br />\r
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/LYCO/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/LYCO/organism-summary?">Summary</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/lycocyc.shtml">More info</a><br /><br />\r
+</td>\r
+<td valign="top" width="35%"><br />\r
+</td>\r
+</tr>\r
+\r
+<tr class="searchbody">\r
+<td colspan="3" rowspan="1" valign="top">\r
+</td>\r
+</tr>\r
+\r
+</table>\r
+* Mirror database. Not curated by the Gramene database. Click on <b>more info</b> link for details.\r
+<br>\r
+\r
+\r
+<h2>Other Tools</h2>\r
+<table width="80%" cellpadding="6" cellspacing="4" align="center">\r
+ <tr class="searchbody">\r
+ <td width="18%"><strong><a href="http://palea.cgrb.oregonstate.edu:1555/expression.html">Omics Viewer</a>: </strong></td>\r
+ <td width="82%" valign="top">Upload and view the realtime mappings of your datasets from microrray expression, proteomics, metabolomics on\r
+Pathway overview diagram</td>\r
+ </tr>\r
+ <tr class="searchbody">\r
+ <td valign="top"><strong><a href="http://palea.cgrb.oregonstate.edu:1555/comp-genomics?comparative=Compare">Comparative analysis</a>: </strong></td>\r
+ <td valign="top">Compare data sets from two or more species for\r
+reactions, pathways, compounds, proteins, transporters and/or transcription units</td>\r
+ </tr>\r
+ </table>\r
+\r
+ <h2>Help </h2>\r
+<table width="80%" cellpadding="6" cellspacing="4" align="center">\r
+ <tr class="searchbody">\r
+ <td width="20%" valign="top"><a href="http://palea.cgrb.oregonstate.edu:1555/serverhelp.shtml"><b>Help</b></a></td>\r
+ <td valign="top">Presents an overview on how to use the pathway database and lists explanations of field names.</td>\r
+ </tr>\r
+ <tr class="searchbody">\r
+ <td valign="top"><a href="/tutorials/pathways_intro"><b>Tutorial</b></a></td>\r
+ <td valign="top">More in-depth than the help pages, use the tutorial for an example of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency. </td>\r
+ </tr>\r
+<!---\r
+ <tr class="searchbody">\r
+ <td valign="top"><b><a href="http://www.gramene.org/db/help?state=display_topic_in_context&topic_name=release_notes">Release Notes</a></b></td>\r
+ <td valign="top">For more information about the most recent release. </td>\r
+ </tr>\r
+--->\r
+\r
+</table>\r
+\r
+ <h2>Quicklink for selected rice pathways </h2>\r
+<table class="searchbody" width="80%" cellpadding="6" cellspacing="4" align="center">\r
+ <tr class="searchbody">\r
+ <td style="vertical-align: top; ">\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=Auxin-Biosynthesis">\r
+ Auxin metabolism </a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=Brassinosteroid-Biosynthesis">\r
+ Brassinosteroid metabolsm</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=CYTOKININ-BIOSYNTHESIS">\r
+ Cytokinin metabolism</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=ETHYL-PWY">\r
+ Ethylene biosynthesis from methionine</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=GIBBERELLIN-SYN">\r
+ Gibberellin metabolism</a><br />\r
+ </td>\r
+ <td style="vertical-align: top;">\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=PWY-735">\r
+ Jasmonic acid biosynthesis</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=PWY-981">\r
+ Salicylic acid biosynthesis</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=Pentose-Phosphate-Cycle">\r
+ Pentose phosphate pathways</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=Photosynthesis">\r
+ Photosynthesis</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=Respiration">\r
+ Respiration</a></td>\r
+\r
+ <td style="vertical-align: top;">\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=SECONDARY-METABOLITE-BIOSYNTHESIS">\r
+ Secondary metabolic pathways</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=PWY-622">\r
+ Starch biosynthesis</a><br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/NEW-IMAGE?object=TCA-VARIANTS">\r
+ TCA cycle</a><br />\r
+ <br />\r
+ <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/class-instances?object=Pathways">\r
+ ALL pathways</a> </td>\r
+ </tr>\r
+</table>\r
+\r
+<a name = "download"></a><h2>Download</h2>\r
+ <ul>\r
+ <li><a href="ftp://ftp.gramene.org/pub/gramene/pathways/">Downloads</a> from our ftp archive.\r
+ <li>For other species, please follow the links from the <a href="#acknowledgements">Acknowledgements</a></li>\r
+ </ul>\r
+\r
+ <h2>Useful external links</h2>\r
+<table width="80%" cellpadding="6" cellspacing="4" align="center">\r
+ <tr>\r
+ <td width="36%" scope="col">\r
+ <a href="http://www.genome.jp/kegg/pathway.html">KEGG pathways</a><br />\r
+ <a href="http://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+gn:T01015">KEGG rice pathways</a><br />\r
+ <a href="http://www.chem.qmul.ac.uk/iubmb/enzyme/">IUBMB Enzyme nomenclature</a><br />\r
+ <a href="http://www.brenda-enzymes.info/">Brenda enzyme database</a><br />\r
+ </td>\r
+ <td width="64%" scope="col">\r
+ <a href="http://www.biocyc.org/">BioCyc</a><br />\r
+ <a href="http://ca.expasy.org/enzyme/">ENZYME at Expasy</a><br />\r
+ <a href="http://www.reactome.org">Reactome</a><br />\r
+ <a href="http://bioinformatics.med.yale.edu/rc/overview.jspx">Cellular Expression Profiling of Rice</a><br />\r
+ <a href="http://www.ricearray.org/">Rice oligonucleotide array project</a><br />\r
+ </td>\r
+ </tr>\r
+ </table></ul>\r
+ <h2>Feedback</h2>\r
+ <ul>\r
+ <p>\r
+ Since the functions of many of the rice genes are either provided by homology\r
+ and HMM based predictions, many of the pathways might be incomplete\r
+ or may contain errors. The manual curation of pathways is an ongoing process at\r
+ Gramene. If you notice any problems or errors on the pathways or would like to\r
+ nominate a pathway for inclusion, please send a message to\r
+ Gramene users on the <a href="mailto:gramene@gramene.org">Gramene list-serve</a>\r
+ or by clicking the '<a href="/db/feedback/send_feedback?refer_from=/pathway/index.html">\r
+ Feedback</a>' button at the bottom of the pathway tools display page.\r
+</P></ul>\r
+\r
+<a name="acknowledgements"></a><h2>Acknowledgements</h2>\r
+<ul>\r
+<p>\r
+ RiceCyc, SorghumCyc, MaizeCyc and BrachyCyc pathway databases were created using the <a href="http://bioinformatics.ai.sri.com/ptools/">Pathway Tools</a> software developed by Peter D. Karp</a> and coworkers in the <a href="http://bioinformatics.ai.sri.com/">Bioinformatics Research Group</a> at SRI International.\r
+</p>\r
+\r
+<p>\r
+ We host mirrors of several species specific plant pathways imported from their original project sites:\r
+<ul>\r
+ <li><i>Arabidopsis thaliana</i> pathways were imported from\r
+ <a href="http://www.arabidopsis.org/biocyc/index.jsp">AraCyc</a> </li>\r
+ <li>PlantCyc pathways were imported from\r
+ <a href="http://www.plantcyc.org/">PlantCyc</a> </li>\r
+ <li> <i>Esherichia. coli</i> pathways were imported from\r
+ <a href="http://www.ecocyc.org">EcoCyc</a></li>\r
+<!--li><i>Capsicum anuum, Coffea canephora, Solanum lycopersicum</i>, and-->\r
+<li><i>Coffea canephora, Solanum lycopersicum</i>, and\r
+ <i>Solanum tuberosum </i> pathways were imported from\r
+ <a href="http://www.sgn.cornell.edu/tools/solcyc/">Sol Genomics Network</a> </li>\r
+ <li>Medicago truncatula pathways were imported from the\r
+ <a href="http://www.noble.org/mediccyc/">The SR Noble foundation</a></li>\r
+ <li><a href="http://www.metacyc.org">MetaCyc pathways</a> were imported as integral part of the Pathway Tools provided by the SRI International</a></li>\r
+</ul></P></ul>\r
+\r
+</blockquote>\r
+</BODY>\r
+</HTML>\r
projects / old-jaiswallab-svn / .git / commitdiff