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云之南

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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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Pathway分析工具  

2010-04-13 22:01:14|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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Pathway分析工具

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.

Thimm, Oliver 1; Blasing, Oliver 1; Gibon, Yves 1; Nagel, Axel 2; Meyer, Svenja 2; Kruger, Peter 1; Selbig, Joachim 1; Muller, Lukas A. 3; Rhee, Seung Y. 3; Stitt, Mark 1,*
(1) Max Planck Institute for Molecular Plant Physiology, Golm, ALLEMAGNE
(2) RZPD German Resource Centre for Genome Research, Heubnerweg 6, 14059 Berlin, ALLEMAGNE
(3) TAIR, The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, Stanford, ALLEMAGNE

Plant Journal. 37(6):914-939, March 2004.

09/16/09 at 10:07:23,在MapMan Software Forum上跟作者联系,通讯作者Marc于09/18/09 at 14:32:42回复:

we can create a glycine max mapping (as there is none yet) using our automated annotation pipeline. To do so we would need sequence information. If you are interested in using the Affymetrix soybean chip i can use the soy targets sequences available from their webpage to create the mapping. If you would like to have a mapping for another set of soybean sequences, please let me know which one you'd prefer.

09/19/09 at 02:54:12,我提供了基因组序列和注释:

The raw sequence data from the genome sequencing projects is on the site: http://www.phytozome.net/soybean

The SoyBase Affymetrix ? GeneChip ? Soybean Genome Array Annotation is on the site: http://soybase.org/AffyChip/index.php.
In this annotation, the Affymetrix Probe set ID has mapped to the genome sequencing ID, AGI, and GO annotation. Maybe they are helpful.

09/28/09 at 12:00:10,Marc回复:

i am working on mappings for both platforms now - as soon as both of them are finished i'll let you know via this forum.

10/02/09 at 14:29:29,Marc回复:

the mapping for the Affymatrix platform is ready and available for download from within mapman. If you need the clear text format file please send my a reply adress and i'll be happy to send it to you.

Gmax_AFFY_09.m02 1.0

感触:遇到问题积极跟作者沟通,老外挺认真的,从开始联系共两周,做出了mapping,效率蛮高。

PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

Bj?rn Usadel1 email, Axel Nagel2 email, Dirk Steinhauser1 email, Yves Gibon1 email, Oliver E Bl?sing1 email, Henning Redestig1 email, Nese Sreenivasulu3 email, Leonard Krall1 email, Matthew A Hannah1 email, Fabien Poree1 email, Alisdair R Fernie1 email and Mark Stitt email

1Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany

2RZPD: Deutsches Ressourcenzentrum für Genomforschung GmbH, Heubnerweg 6, 14059 Berlin, Germany

3Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany

BMC Bioinformatics 2006, 7:535doi:10.1186/1471-2105-7-535

Extending MapMan: application to legume genome arrays

Nicolas Goffard and Georg Weiller *

ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University GPO Box 475, Canberra, ACT 2601, Australia

Bioinformatics 2006 22(23):2958-2959; doi:10.1093/bioinformatics/btl517

扩展到大豆和苜蓿,可是maping文件只有苜蓿的,未见大豆的,可以在GeneBins的Download处下载Pathway Pictures & XML annotation。另外,人性化的map文本是可以通过email获得,还未向所有人公开。

GeneBins: a database for classifying gene expression data, with application to plant genome arrays

Nicolas Goffard email and Georg Weiller email

ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia

BMC Bioinformatics 2007, 8:87doi:10.1186/1471-2105-8-87

Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula

用到了上面的Extending MapMan,扩展到拟南芥、大豆、苜蓿、水稻。

PathExpress: a web-based tool to identify relevant pathways in gene expression data

Nicolas Goffard and Georg Weiller*

ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601 Australia

Nucleic Acids Research 2007 35(Web Server issue):W176-W181; doi:10.1093/nar/gkm261

 

应用举例:

GeneBins

Overlap of Proteome Changes in Medicago truncatula in Response to Auxin and Sinorhizobium meliloti1,[W],[OA]

Giel E. van Noorden, Tursun Kerim, Nicolas Goffard, Robert Wiblin, Flavia I. Pellerone, Barry G. Rolfe and Ulrike Mathesius*

Australian Research Council Centre of Excellence for Integrative Legume Research (G.E.v.N., N.G., F.I.P., B.G.R., U.M.), Genomic Interactions Group, Research School of Biological Sciences (G.E.v.N., T.K., N.G., B.G.R.), and School of Biochemistry and Molecular Biology (G.E.v.N., T.K., R.W., F.I.P., U.M.), Australian National University, Canberra, Australian Capital Territory 0200, Australia

本文引用地址: http://www.sciencenet.cn/m/user_content.aspx?id=255956


BiblioSphere
http://www.bio-soft.net/other/BiblioSpherePE.htm
DAVID 6.7
http://david.abcc.ncifcrf.gov/

ingenuity Pathway Analysis
http://www.ingenuity.com/
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