Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

Table 2 Clustering simulation analysis of co-expressed genes (50 kb window) in ES and PES internodes of alfalfa genotypes 252 and 1283.

Gene Category*	Tissue Type	Number of Genes^†	Simulation Mean^‡	Simulation SD	Experimental Data^§	SD from Simulation Mean^¶
up in 252	ES	1.0	192.8	5.3	163.0	-5.6
		2.0	7.7	2.6	16.0	3.2
		3.0	1.0	0.4	3.0	5.6
down in 252	ES	1.0	212.4	5.9	189.0	-4.0
		2.0	9.2	2.8	13.0	1.3
		3.0	1.2	0.5	3.0	3.7
up in 252	PES	1.0	309.5	8.3	262.0	-5.7
		2.0	20.3	4.0	34.0	3.4
		3.0	1.7	0.9	4.0	2.6
		4.0	1.0	0.1	3.0	20.0
down in 252	PES	1.0	354.3	9.5	307.0	-5.0
		2.0	26.9	4.5	46.0	4.3
		3.0	2.1	1.2	5.0	2.4

*Genes up- or down-regulated in genotype 252 compared to genotype 1283.
^†Number of genes identified within the 50 kb bin of the simulation.
^‡Average number of bins with the corresponding gene numbers from replicated simulation (×2000).
^§Number of 50 kb bins with the corresponding gene number from this study.
^¶(Experimental Data - Simulation Mean)/(Simulation SD). Value of 2 or greater indicates statistically significant clustering of genes.

ISSN: 1471-2164