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Open Access Highly Accessed Research article

Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis

Ping Lan12*, Wenfeng Li2 and Wolfgang Schmidt2

Author Affiliations

1 State Key Laboratory of Soil and Sustainable Agriculture,Institute of Soil Science, Chinese Academy Sciences, Nanjing, 210008, People’s Republic of China

2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan

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BMC Genomics 2013, 14:210  doi:10.1186/1471-2164-14-210

Published: 1 April 2013

Additional files

Additional file 1:

Expression of 1,118 kinase genes in Arabidopsis retrieved from TAIR10 roots.

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Additional file 2:

Expression of 205 phosphatase genes in Arabidopsis roots retrieved from TAIR10.

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Additional file 3:

Distribution of transcripts derived from protein kinase genes in Arabidopsis roots.

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Additional file 4:

432 PK and 85 PP proteins identified in Arabidopsis roots.

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Additional file 5:

Expression of the cysteine-rich RLK (receptor-like protein kinase) subfamily in Arabidopsis roots.

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Additional file 6:

GO enrichment analysis of the 57 highly expressed protein kinase genes in Arabidopsis roots.

Format: XLSX Size: 24KB Download file

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Additional file 7:

A subset of 29 protein phosphatase genes not or lowly expressed in Arabidopsis roots.

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Additional file 8:

GO enrichment analysis of the subset of 29 protein phosphatase not or lowly expressed genes in Arabidopsis roots.

Format: XLS Size: 18KB Download file

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Additional file 9:

GO enrichment analysis of the subset of nine protein phosphatase genes with high abundance in Arabidopsis roots.

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Additional file 10:

Subsets of 173 PK and 35 PP genes, comprising diverse subfamilies that were differentially expressed under Pi-deficient conditions in Arabidopsis roots.

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Additional file 11:

GO enrichment analysis 205 protein kinase and phosphatase genes upon Pi deficiency in Arabidopsis roots.

Format: XLSX Size: 87KB Download file

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Additional file 12:

Digital expression information of the 29 purple acid phosphatase genes in Arabidopsis roots.

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Additional file 13:

Co-expression relationships of protein kinase and phosphatase genes upon Pi deficiency in Arabidopsis roots. Red nodes indicate up-regulated genes, green nodes denote genes that are repressed by Pi deficiency. Round-shaped nodes represent protein kinase genes, rectangles indicate protein phosphatase genes.

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Additional file 14:

Genes comprising the PK/PP co-expression network in Arabidopsis roots.

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Additional file 15:

GO enrichment analysis of 65 PK and PP genes involved in Co-expression network.

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Additional file 16:

GO enrichment analysis of the 22 genes comprising the co-expression network PKPP1.

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Additional file 17:

Protein-protein interaction pairs and statistics of edge enrichment for the co-expression network REPKPP1.

Format: XLSX Size: 323KB Download file

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Additional file 18:

A subset of 75 Genes from the root epidermal ‘core’ genes fished for the co-expression network in Arabidopsis roots.

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Additional file 19:

GO enrichment analysis of the six fished genes involved in the co-expression network REPKPP1A.

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Additional file 20:

GO enrichment analysis of the 69 fished genes involved in the co-expression network REPKPP1B.

Format: XLS Size: 21KB Download file

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