Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes

doi:10.1002/0471250953.bi0111s30

. 2010 Jun:Chapter 1:1.11.1-1.11.51.

doi: 10.1002/0471250953.bi0111s30.

Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes

Philippe Lamesch¹, Kate Dreher¹, David Swarbreck¹, Rajkumar Sasidharan¹, Leonore Reiser¹, Eva Huala¹

Affiliations

PMID: 20521243
DOI: 10.1002/0471250953.bi0111s30

Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes

Philippe Lamesch et al. Curr Protoc Bioinformatics. 2010 Jun.

. 2010 Jun:Chapter 1:1.11.1-1.11.51.

doi: 10.1002/0471250953.bi0111s30.

Authors

Philippe Lamesch¹, Kate Dreher¹, David Swarbreck¹, Rajkumar Sasidharan¹, Leonore Reiser¹, Eva Huala¹

Affiliation

¹ Carnegie Institution for Science, Stanford, California.

PMID: 20521243
DOI: 10.1002/0471250953.bi0111s30

Abstract

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, biochemical pathways, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and describes several new tools such as a new TAIR genome browser (GBrowse), and the TAIR synteny viewer (GBrowse_syn). We also describe how to use AraCyc for mining plant metabolic pathways.

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References

Literature Cited

1. Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
1. Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.A., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., and Rhee, S.Y. 2004. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135:745-755.
1. Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., and Hubbard, T. 2004. Ensembl 2004. Nucleic Acids Res. 32:D468-D470.
1. Borevitz, J.O. and Nordborg, M. 2003. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 132:718-725.
1. Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds, D.A., Chen, H., Frazer, K.A., Huson, D.H., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J.R., and Weigel, D. 2007. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338-342.

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[1] Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.

[2] Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.

[3] Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.A., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., and Rhee, S.Y. 2004. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135:745-755.

[4] Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., Mueller, L.A., Yoon, J., Doyle, A., Lander, G., Moseyko, N., Yoo, D., Xu, I., Zoeckler, B., Montoya, M., Miller, N., Weems, D., and Rhee, S.Y. 2004. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135:745-755.

[5] Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., and Hubbard, T. 2004. Ensembl 2004. Nucleic Acids Res. 32:D468-D470.

[6] Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., and Hubbard, T. 2004. Ensembl 2004. Nucleic Acids Res. 32:D468-D470.

[7] Borevitz, J.O. and Nordborg, M. 2003. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 132:718-725.

[8] Borevitz, J.O. and Nordborg, M. 2003. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 132:718-725.

[9] Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds, D.A., Chen, H., Frazer, K.A., Huson, D.H., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J.R., and Weigel, D. 2007. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338-342.

[10] Clark, R.M., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds, D.A., Chen, H., Frazer, K.A., Huson, D.H., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J.R., and Weigel, D. 2007. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338-342.

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Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes

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Using the Arabidopsis information resource (TAIR) to find information about Arabidopsis genes

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