List of useful Datasets - Revision history

Cooperl: /* Rice Gene Expression Atlas (Wang et al, 2010) */

2011-07-20T20:18:01Z

Rice Gene Expression Atlas (Wang et al, 2010)

Cooperl: /* Rice Gene Expression Atlas (Wang et al, 2010) */

2011-07-20T20:17:12Z

Rice Gene Expression Atlas (Wang et al, 2010)

Cooperl: /* Other sources of micorarray data: */

2011-01-28T00:28:22Z

Other sources of micorarray data:

Cooperl: /* Other sources of micorarray data: */

2011-01-28T00:27:45Z

Other sources of micorarray data:

Cooperl: /* Other sources of micorarray data: */

2011-01-27T23:04:55Z

Other sources of micorarray data:

Cooperl: /* Other sources of micorarray data: */

2011-01-27T23:04:11Z

Other sources of micorarray data:

Cooperl: /* Other sources of micorarray data: */

2010-12-07T21:03:20Z

Other sources of micorarray data:

Cooperl: /* Other sources of micorarray data: */

2010-12-07T21:00:35Z

Other sources of micorarray data:

Rwalls: /* gymnosperm EST data sets */

2010-12-07T13:11:05Z

gymnosperm EST data sets

Rwalls: /* Other sources of micorarray data: */

2010-12-07T12:05:15Z

Other sources of micorarray data:

@@ Line 23: / Line 23: @@
 *[http://www.affymetrix.com/browse/products.jsp?productId=131497&navMode=34000&navAction=jump&aId=productsNav#1_1 Affymetrics GeneChip® Rice Genome Array ]
--contains 57,381 probe sets in total, of which 1347 represent 1260 transcripts of an indica variety and 54 168 represent 48 564 transcripts of a japonica variety.
+-contains 57,381 probe sets in total, of which 1347 represent 1260  indica transcripts and 54 168 represent 48 564 japonica transcripts.
 *31 tissues/organs from throughout the plant life cycle,from two ''indica'' varieties; Zhenshan 97 and Minghui 63.

@@ Line 24: / Line 24: @@
 *[http://www.affymetrix.com/browse/products.jsp?productId=131497&navMode=34000&navAction=jump&aId=productsNav#1_1 Affymetrics GeneChip® Rice Genome Array ]
 -contains 57,381 probe sets in total, of which 1347 represent 1260 transcripts of an indica variety and 54 168 represent 48 564 transcripts of a japonica variety.
 *31 tissues/organs from throughout the plant life cycle,from two ''indica'' varieties; Zhenshan 97 and Minghui 63.

← Older revision		Revision as of 00:28, 28 January 2011
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	[http://affymetrix.arabidopsis.info/ NASCArrays]		[http://affymetrix.arabidopsis.info/ NASCArrays]

		+	NASCArrays is the Nottingham Arabidopsis Stock Centre's microarray database. Currently we hybridise over 1000 GeneChips per year mostly for Arabidopsis thaliana experiments which we make public, more than from any other GeneChip centre. There are also experiments from other species, and experiments run by other centres.

	Need to find datasets for Gymnosperms/lower plants/ non-model-organisms		Need to find datasets for Gymnosperms/lower plants/ non-model-organisms

@@ Line 116: / Line 116: @@
 [http://cibex.nig.ac.jp/index.jsp CIBEX]
 CIBEX is a public database for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED Society recommendations.
 Need to find datasets for Gymnosperms/lower plants/ non-model-organisms

@@ Line 115: / Line 115: @@
 [http://cibex.nig.ac.jp/index.jsp CIBEX]
+CIBEX is a public database for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED Society recommendations.
 Need to find datasets for Gymnosperms/lower plants/ non-model-organisms

← Older revision		Revision as of 23:04, 27 January 2011
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	PlantTribes 1.0 incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments [link to the doc page]. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences.		PlantTribes 1.0 incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments [link to the doc page]. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences.

		+
		+	[http://cibex.nig.ac.jp/index.jsp CIBEX]


	Need to find datasets for Gymnosperms/lower plants/ non-model-organisms		Need to find datasets for Gymnosperms/lower plants/ non-model-organisms

← Older revision		Revision as of 21:03, 7 December 2010
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		+	-[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb2/ Virtual Plant]
		+
		+	* VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.

−	~~Need to find datasets for Gymnosperms/lower plants/ non-model-organisms~~

		+	'''List of microarray data sources on TAIR:''' http://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp

−	~~-[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb2/ Virtual Plant]~~

−	* VirtualPlant integrates genomic data ~~and provides visualization and analysis tools~~ for ~~rapid~~ and ~~efficient exploration~~ of ~~genomic data~~. ~~The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses~~.	+	'''[http://fgp.huck.psu.edu/tribedb/index.pl PlantTribes]
		+	'''
		+	PlantTribes is an objective classification system for plan proteins based on cluster analyses of the inferred proteomes of the sequenced angiosperms Arabidopsis thaliana v Columbia, Oryza sativa v. japonica (Rice), and Populus trichocarpa (poplar). Sequence data for Carica papaya (papaya v. 1.0; R. Ming et al. in preparation) and Medicago papaya (barrel medic, 60% complete) are also included in the current version of Tribes (v. 1.0).

		+	PlantTribes 1.0 incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments [link to the doc page]. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences.

−	~~'''List of microarray data sources on TAIR:''' http://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp~~


−	~~[http:~~//~~fgp.huck.psu.edu/tribedb/index.pl Plant Tribes]~~	+	Need to find datasets for Gymnosperms/lower plants/ non-model-organisms

← Older revision		Revision as of 21:00, 7 December 2010
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	'''List of microarray data sources on TAIR:''' http://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp		'''List of microarray data sources on TAIR:''' http://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp
		+
		+
		+	[http://fgp.huck.psu.edu/tribedb/index.pl Plant Tribes]

@@ Line 65: / Line 65: @@
 -It can be searched by querying single gene or multiple genes using gene sequences, gene names, or the probe identifications, for items like quantified expression values, the co-expressed genes, the tissues and varieties in which they are expressed.
-==gymnosperm EST data sets==
+==gymnosperm data sets==
-EST sequences for Gingko biloba and Cycas rumphii: http://www.ncbi.nlm.nih.gov/sra/SRP002638
+* EST sequences for Gingko biloba and Cycas rumphii: http://www.ncbi.nlm.nih.gov/sra/SRP002638
 May not be that useful; just contains the sequences.
 ==Other sources of micorarray data:==

← Older revision		Revision as of 12:05, 7 December 2010
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	* VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.		* VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.
		+
		+
		+	'''List of microarray data sources on TAIR:''' http://www.arabidopsis.org/portals/expression/microarray/microarrayDatasetsV2.jsp