From: pankaj Date: Thu, 20 Mar 2014 21:06:45 +0000 (+0000) Subject: metabolic pathway database and species listing X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=7eaba35b46745e79302c9bd797b9c2089ed27f3d;p=old-jaiswallab-svn%2F.git metabolic pathway database and species listing svn path=/; revision=542 --- diff --git a/pathways/html/metabolic.html b/pathways/html/metabolic.html new file mode 100644 index 0000000..9243147 --- /dev/null +++ b/pathways/html/metabolic.html @@ -0,0 +1,253 @@ + + + + + + + + + + + +

+ +
Plant Metabolic Pathways
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
RiceCyc ver 3.3
+Oryza sativa japonica
+Strain: Nipponbare
Browse | Summary | More info
+ AraCyc* ver 10.0
+Arabidopsis thaliana
+Strain: Columbia
Browse | Summary | More info
+ EcoCyc* ver 17.0
+Escherichia coli
+Strain: K-12 MG1655
Browse | Summary | More info

+
SorghumCyc ver 1.1
+Sorghum bicolor
+Strain: BTx623
Browse | Summary | More info

+ MedicCyc* ver 1.0.1
+Medicago truncatula, Barrelclover
+Unavailable
Browse | Summary | More info

+ MetaCyc* ver 17.0
+Reference Pathway Database
+Strain: not applicable
Browse | Summary | More info

+
MaizeCyc ver 2.1
+Zea mays
+Strain: B73
Browse | Summary | More info

+ PoplarCyc* ver 5.0
+Populus trichocarpa (and other Populus species and hybrids)
+Strain: n/a
Browse | Summary | More info

+ PlantCyc* ver 7.0
+Plant Metabolic Pathway Database
+Strain: not applicable
Browse | Summary | More info

+
BrachyCyc ver 2.0
Brachypodium distachyon
+Strain: Bd21
Browse | Summary | More info

+ PotatoCyc* ver 1.0.1
+Solanum tuberosum, Potato
+Strain: n/a
Browse | Summary | More info

+
+

+ CoffeaCyc* ver 1.1.1
+Coffea canephora, Coffee
+Strain: n/a
Browse | Summary | More info

+
+

+ LycoCyc* ver 2.0.1
+Solanum lycopersicum, Tomato
+Strain: n/a
Browse | Summary | More info

+
+
+
+* Mirror database. Not curated by the Gramene database. Click on more info link for details. +
+ + +
Other Tools
+ + + + + + + + + +
Omics Viewer: Upload and view the realtime mappings of your datasets from microrray expression, proteomics, metabolomics on +Pathway overview diagram
Comparative analysis: Compare data sets from two or more species for +reactions, pathways, compounds, proteins, transporters and/or transcription units
+ +
Help
+ + + + + + + + + + + +
Help Presents an overview on how to use the pathway database and lists explanations of field names.
Tutorial 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.
+ +
Quicklink for selected rice pathways
+ + + + + + + +
+ + Auxin metabolism
+ + Brassinosteroid metabolsm
+ + Cytokinin metabolism
+ + Ethylene biosynthesis from methionine
+ + Gibberellin metabolism
+ + + Jasmonic acid biosynthesis
+ + Salicylic acid biosynthesis
+ + Pentose phosphate pathways
+ + Photosynthesis
+ + Respiration + + Secondary metabolic pathways
+ + Starch biosynthesis
+ + TCA cycle
+
+ + ALL pathways
+ +
Download
+
+
Downloads from our ftp archive. +
For other species, please follow the links from the Acknowledgements
+
+ +
Useful external links
+ + + + + +
+ KEGG pathways
+ KEGG rice pathways
+ IUBMB Enzyme nomenclature
+ Brenda enzyme database
+ + BioCyc
+ ENZYME at Expasy
+ Reactome
+ Cellular Expression Profiling of Rice
+ Rice oligonucleotide array project
+
+
Feedback
+
+
+ Since the functions of many of the rice genes are either provided by homology + and HMM based predictions, many of the pathways might be incomplete + or may contain errors. The manual curation of pathways is an ongoing process at + Gramene. If you notice any problems or errors on the pathways or would like to + nominate a pathway for inclusion, please send a message to + Gramene users on the Gramene list-serve + or by clicking the ' + Feedback' button at the bottom of the pathway tools display page. +
+ +
Acknowledgements
+
+
+ RiceCyc, SorghumCyc, MaizeCyc and BrachyCyc pathway databases were created using the Pathway Tools software developed by Peter D. Karp and coworkers in the Bioinformatics Research Group at SRI International. +
+ +
+ We host mirrors of several species specific plant pathways imported from their original project sites: +
+
Arabidopsis thaliana pathways were imported from + AraCyc
+
PlantCyc pathways were imported from + PlantCyc
+
Esherichia. coli pathways were imported from + EcoCyc
+ +
Coffea canephora, Solanum lycopersicum, and + Solanum tuberosum pathways were imported from + Sol Genomics Network
+
Medicago truncatula pathways were imported from the + The SR Noble foundation
+
MetaCyc pathways were imported as integral part of the Pathway Tools provided by the SRI International
+
+ +

+ +

RiceCyc ver 3.3 +Oryza sativa japonica +Strain: Nipponbare Browse \| Summary \| More info +	AraCyc* ver 10.0 +Arabidopsis thaliana +Strain: Columbia Browse \| Summary \| More info +	EcoCyc* ver 17.0 +Escherichia coli +Strain: K-12 MG1655 Browse \| Summary \| More info +
SorghumCyc ver 1.1 +Sorghum bicolor +Strain: BTx623 Browse \| Summary \| More info +	MedicCyc* ver 1.0.1 +Medicago truncatula, Barrelclover +Unavailable Browse \| Summary \| More info +	MetaCyc* ver 17.0 +Reference Pathway Database +Strain: not applicable Browse \| Summary \| More info +
MaizeCyc ver 2.1 +Zea mays +Strain: B73 Browse \| Summary \| More info +	PoplarCyc* ver 5.0 +Populus trichocarpa (and other Populus species and hybrids) +Strain: n/a Browse \| Summary \| More info +	PlantCyc* ver 7.0 +Plant Metabolic Pathway Database +Strain: not applicable Browse \| Summary \| More info +
BrachyCyc ver 2.0 Brachypodium distachyon +Strain: Bd21 Browse \| Summary \| More info +	PotatoCyc* ver 1.0.1 +Solanum tuberosum, Potato +Strain: n/a Browse \| Summary \| More info +	+
+	CoffeaCyc* ver 1.1.1 +Coffea canephora, Coffee +Strain: n/a Browse \| Summary \| More info +	+
+	LycoCyc* ver 2.0.1 +Solanum lycopersicum, Tomato +Strain: n/a Browse \| Summary \| More info +	+
+

Omics Viewer:	Upload and view the realtime mappings of your datasets from microrray expression, proteomics, metabolomics on +Pathway overview diagram
Comparative analysis:	Compare data sets from two or more species for +reactions, pathways, compounds, proteins, transporters and/or transcription units

Help	Presents an overview on how to use the pathway database and lists explanations of field names.
Tutorial	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.