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Open Access Research article

Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria

Jiangxin Wang12, Gang Wu3, Lei Chen12 and Weiwen Zhang12*

Author Affiliations

1 School of Chemical Engineering & Technology, Tianjin University, 300072, Tianjin, People's Republic of China

2 Key Laboratory of Systems Bioengineering, Ministry of Education, 300072, Tianjin, People's Republic of China

3 Department of Biological Sciences, University of Maryland at Baltimore County, 21250, Baltimore, MD, USA

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BMC Genomics 2013, 14:112  doi:10.1186/1471-2164-14-112

Published: 19 February 2013

Additional files

Additional file 1: Figure S1:

Clustering of the transcriptomic datasets under iron and copper treatments in different species. The grouped datasets with solid red color in “HighCopper” and “Iron” suggested high confident grouping of treated groups from controls.

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Additional file 2: Figure S2:

Association between phenotypes and identified transcriptional modules in different species. Each of the identified transcriptional modules was indicated by different colors, and their association with the phenotypes was indicated by p-values.

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Additional file 3: Figure S3:

Overlap of the detected responsive modules within and between cyanobacteria species. The lines connected different cyanobacteria species means there are some genes shared between specific modules.

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Additional file 4: Table S1:

genes and pathways in SYW-yellow module.

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Additional file 5: Table S2:

genes and pathways in SYW-Green yellow module.

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Additional file 6: Table S3:

genes and pathways in SYG-dark green module.

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Additional file 7: Table S4:

genes and pathways in SYG-brown module.

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Additional file 8: Figure S4:

Shared responsive genes in cyanobacteria species to iron depletion and copper toxicity treatments, respectively, and shared responsive genes between treatments in all cyanobacteria species. Nine shared genes among all 4 cyanobacteria species were listed in Table 3.

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Additional file 9: Table S5:

shared genes in iron treatments. The color of each gene indicates differential change: red is up-regulated and green is down-regulated.

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Additional file 10: Table S6:

shared signature genes in copper treatments. The color of each gene indicates the differential change, red is up-regulated and green is down-regulated.

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Additional file 11: Table S7:

Pathways shared in all 4 species.

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Additional file 12: Table S8:

Hub genes with known functions in different cyanobacteria species. The same color from KO_ID and the gene names indicate the hub genes in each species.

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Additional file 13: Table S9:

Hub genes with unknown functions in different cyanobacteria species.

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Additional file 14: Figure S5:

Hierarchical clustering tree using the topological overlap dissimilarity. Tree branches have been colored by module membership. A, B) PMT, PMM to iron, respectively; C, D) SYW, SYG to copper, respectively. Please refer the text for details of the analysis.

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