Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease

Rawat, Nidhi; Kiran, Sandhya P.; Du, Dongliang; Gmitter, Fred G.; Deng, Zhanao

doi:10.1186/s12870-015-0568-4

Table 1 Details of microarray studies used for meta-analysis

From: Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease

Dataset	Designated in present analysis	Reference	Genotype	Number of samples	Tissue	Time after CaLas infection	GSE Dataset	Analysis method	Analysis statistic	Up-regulated Probesets	Down- regulated Probesets
Root dataset	Valencia root	[3]	Valencia	6 (3C^f + 3I^f)	Root	16 months	GSE33004	Limma R Package	Unadjusted P < 0.05 FC > 2	56	55
Stem dataset	Valencia stem	[3]	Valencia	6 (3C + 3I)	Stem	16 months	GSE33004	Limma R Package	Unadjusted P < 0.05 FC > 2	551	334
Susceptible (S) leaf dataset	Valencia 5–9 wai^a	[1]	Valencia	5 (2C + 3I)	Leaf	5-9 week	GSE33459	local pooled Error (LPE)	Adjusted P (FDR < 0.05) FC > 2	195	84
	Valencia 13–17 wai	[1]	Valencia	5 (2C + 3I)	Leaf	13-17 week	GSE33459	local pooled Error (LPE)	Adjusted P (FDR < 0.05) FC > 2	310	205
	Sweet orange	[31]	sweet orange	6 (3C + 3I)	Leaf	8 months	GSE33003	Limma R Package	Unadjusted P < 0.05 FC > 2	307	317
	Madam Vinous	[18]	Madam Vinous	6 (3C + 3I)	Leaf	7 months	GSE29633	Limma R Package	Unadjusted P < 0.05 FC > 2	943	1060
	Cleopatra	[2]	Cleopatra	6 (3C + 3I)	Leaf	32 week	GSE30502	Partek suit two way ANOVA	Adjusted P (FDR < 0.05) FC > 4	326	68
	Madam Vinous 5 wai	[19]	Madam Vinous	6 (3C + 3I)	Leaf	5 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	83	101
	Madam Vinous 17 wai	[19]	Madam Vinous	6 (3C + 3I)	Leaf	17 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	614	414
	Madam Vinous 27 wai	[19]	Madam Vinous	6 (3C + 3I)	Leaf	27 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	1955	1523
Resistant (R) leaf dataset	RL^b 5 wai	[19]	Rough Lemon	6 (3C + 3I)	Leaf	5 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	239	447
	RL 17 wai	[19]	Rough Lemon	6 (3C + 3I)	Leaf	17 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	260	154
	RL 27 wai	[19]	Rough Lemon	6 (3C + 3I)	Leaf	27 week	Not available	Limma R Package	Unadjusted P < 0.05 FC > 2	867	190
	US-897	[2]	US-897	6 (3C + 3I)	Leaf	32 week	GSE30502	Partek suit two way ANOVA	Adjusted P (FDR < 0.05) FC > 4	17	none
Fruit dataset	Immature fruit	[40]	Valencia	10 (5C + 5I)	Fruit	_	SRP022979	DESeq package	_	45	24
	Mature fruit	[40]	Valencia	10 (5C + 5I)	Fruit	_	SRP022979	DESeq package	_	234	73
	Hamlin_JV^c	[34]	Hamlin	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	174	116
	Hamlin_VT^d	[34]	Hamlin	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	398	471
	Hamlin_FF^e	[34]	Hamlin	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	696	706
	Valencia_JV	[34]	Valencia	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	291	110
	Valencia_VT	[34]	Valencia	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	288	257
	Valencia_FF	[34]	Valencia	8 (4C + 4I)	Fruit	_	GSE33373	Limma R Package	Adjusted P (FDR < 0.01) FC > 2	210	324

^aweeks after inoculation, ^bRough Lemon, ^cJuice Vesicle, ^dVascular Tissue, ^eFlavedo, ^fControl and Infected

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ISSN: 1471-2229

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