An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

doi:10.1186/1752-0509-2-31

BMC Systems Biology

Volume 2

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Thum KE
Shin MJ
Gutiérrez RA
Mukherjee I
Katari MS
Nero D
Shasha D
Coruzzi GM

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Shin MJ
Gutiérrez RA
Mukherjee I
Katari MS
Nero D
Shasha D
Coruzzi GM
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Research article

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

Karen E Thum¹ , Michael J Shin¹^,2 , Rodrigo A Gutiérrez¹^,3 , Indrani Mukherjee¹ , Manpreet S Katari¹ , Damion Nero¹ , Dennis Shasha⁴ and Gloria M Coruzzi¹

¹Department of Biology, New York University, New York, NY, 10003, USA

²Department of Biology, Messiah College, Grantham, PA, 17027, USA

³Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile. Alameda 340. 8331010. Santiago, Chile

⁴Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA

author email corresponding author email

BMC Systems Biology 2008, 2:31doi:10.1186/1752-0509-2-31


Published:	4 April 2008

Additional files

Additional file 1:

Metric classes and the genes within each class. A list of 1,625 filtered genes and their 'metric' classification for L/C regulated genes in wild-type and cli186.

Format: XLS Size: 88KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Genes L/C regulated in wild-type and misregulated in cli186. List of genes and gene annotations classified as being 'regulated' in wild-type and cli186 or 'misregulated' in cli186 according to 'metric' classification.

Format: XLS Size: 106KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Patterns of L/C misregulation in cli186. Table showing patterns of misregulation observed among the 216 misregulated genes in cli186.

Format: XLS Size: 12KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

ANOVA analysis. Lists of regulated and misregulated genes as determined via 3-way ANOVA analysis.

Format: XLS Size: 231KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Multinetwork of L/C regulated genes in wild-type. Metabolic and regulatory network created using the Arabidopsis Multinetwork Tool [21], using the 966 L/C regulated set of genes and visualized with Cytoscape [54].

Format: JPEG Size: 3.4MB Download file

Additional file 6:

Supernode network of misregulated genes in cli186. Supernode network created from the 216 misregulated genes in cli186.

Format: JPEG Size: 3MB Download file

Additional file 7:

Misregulated multinetwork in cli186. Metabolic and regulatory network created using the Arabidopsis Multinetwork Tool [21], using the 216 L/C misregulated set of genes from cli186 and visualized with Cytoscape [54].

Format: JPEG Size: 3MB Download file

Additional file 8:

Metric classification. Examples of 'metric classification' system designed to determine L. LC, C misregulated genes in cli186.

Format: XLS Size: 109KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 9:

Q-PCR validation. q-PCR validation of misregulation of HAT22 and its target genes.

Format: PPT Size: 32KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer