Table 1

Assignment of upregulated and downregulated genes in each functional group identified in PPV-infected Arabidopsis leaves and protoplasts.

S.No

Functional category

Number of genes on the array a

PPV-infected leaves Upregulated/Downregulated [Number (%)/Number (%)] b

pPPV-SK68-transfected protoplasts Upregulated/Downregulated [Number (%)/Number (%)] b


A

Defence and virulence

1488

204 (13.7)/165 (11.1)

32 (2.15)/33 (2.22)

B

Cellular communication/Signal transduction mechanism/transmembrane signal transduction

1657

94 (5.67)/74 (4.47)

16 (0.97)/18 (1.09)

C

Cell Cycle/DNA processing/chromatin regulation and cytoskeleton reorganization

771

87 (11.3)/30 (3.89)

10 (1.30)/9 (1.17)

D

Development/storage proteins

657

138 (21)/100 (15.2)

20 (3.04)/20 (3.04)

E

Metabolism

4238

548 (12.9)/226 (5.3)

35 (0.83)/41 (0.97)

F

Proteins with binding function or cofactor requirement

921

210 (22.8)/139 (15.1)

20 (2.17)/22 (2.39)

G

Protein synthesis and translation

314

37 (11.8)/39 (12.4)

1 (0.32)/1 (0.32)

H

Protein fate

647

77 (11.9)/69 (10.6)

9 (1.39)/12 (1.85)

I

Transcription/splicing/RNA processing/modification

1013

175 (17.3)/102 (10.1)

32 (3.16)/29 (2.86)

J

Transporters

563

78 (13.9)/19 (3.4)

7 (1.24)/7 (1.24)

K

Transposable elements, viral and plasmid proteins

124

22 (17.7)/44 (35.5)

8 (6.45)/21 (16.94)

L

Unknown proteins

10417

343 (3.3)/450 (4.3)

73 (0.70)/91 (0.87)


a Number of genes in a given category represented on the chip.

b Percentage was calculated based on the number of differentially regulated genes divided by the total number of genes in the functional category on the chip.

Babu et al. BMC Genomics 2008 9:325   doi:10.1186/1471-2164-9-325

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