Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32432	0.205
27DAP/17DAP	1.19881	0.849
39DAP/27DAP	2.38929	0.119
41DAP/39DAP	1.40864	0.753
42DAP/41DAP	1.05375	1
43DAP/42DAP	1.20857	1
47DAP/43DAP	0.4285	0.049
52DAP/47DAP	0.94768	0.837
57DAP/52DAP	1.15657	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68812	0.035
17DAP/reference	0.72065	0.018
27DAP/reference	0.74714	0.03
39DAP/reference	0.65367	0.016
41DAP/reference	0.67773	0.021
42DAP/reference	1.15773	0.241
43DAP/reference	0.83943	0.135
47DAP/reference	0.87762	0.06
52DAP/reference	0.97624	0.427
57DAP/reference	1.13224	0.114

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86525	0.363
27DAP/17DAP	0.88941	0.132
39DAP/27DAP	1.42912	0.151
41DAP/39DAP	3.57978	0.006
42DAP/41DAP	0.64833	0.011
43DAP/42DAP	0.47984	0.022
47DAP/43DAP	1.03673	0.873
52DAP/47DAP	1.41651	0.474
57DAP/52DAP	0.68652	0.283
57DAP/7DAP	0.77433	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77788	0.072
17DAP/reference	1.83604	0.147
27DAP/reference	1.86698	0.131
39DAP/reference	1.7116	0.186
41DAP/reference	1.0038	0.811
42DAP/reference	1.5505	0.233
43DAP/reference	0.9744	0.48
47DAP/reference	1.2619	0.139
52DAP/reference	1.70813	0.008
57DAP/reference	2.10165	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65173	0.009
17DAP/reference	0.69305	0.004
27DAP/reference	1.05349	0.933
39DAP/reference	1.37466	0.046
41DAP/reference	1.14341	0.094
42DAP/reference	1.22354	0.17
43DAP/reference	1.43517	0.655
47DAP/reference	1.39736	0.128
52DAP/reference	1.03849	0.747
57DAP/reference	1.83455	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12477	0.377
17DAP/reference	1.1293	0.602
27DAP/reference	0.85026	0.063
39DAP/reference	1.30765	0.12
41DAP/reference	1.39011	0.043
42DAP/reference	1.2309	0.099
43DAP/reference	1.16152	0.426
47DAP/reference	0.66681	0.005
52DAP/reference	0.9668	0.663
57DAP/reference	1.21872	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.65915	0.966
26DAP/20DAP	0.83514	0.512
34DAP/26DAP	1.03792	1
51DAP/34DAP	0.70202	0.141
52DAP/51DAP	1.38984	0.439
53DAP/52DAP	0.93833	0.767
55DAP/53DAP	1.36478	0.185
57DAP/55DAP	0.70857	0.046
62DAP/57DAP	1.01665	1
68DAP/62DAP	1.24209	0.481
68DAP/14DAP	1.28297	0.469

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.23488	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	16.2804	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.50348
12-2/M82	0.70709	0.955
12-4/M82	0.7043
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.85097
3-2/M82	N/A	N/A
4-1-1/M82	4.22403	0.782
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	2.13111	0.572
6-2/M82	16.2537	0.253
6-3/M82	0.35905
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.80187

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69156	0.243
IL2-6/WTpooled	1.0997	0.584
IL7-5/WTpooled	1.09545	1
IL7-3/WTpooled	1.14547	1
IL12-4/WTpooled	0.75024	0.554
IL1-4/WTpooled	1.01824	1
WT/WTpooled	1.00193	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.62636	0.699

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91131	1
DC3000/delta hrp 6h	1.08856	1
DC3000/delta hrp 12h	0.86615	1
DC3000/delta hrp 24h	1.39702	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.27519	0.134
DC3000 delta B/DC3000 delta AB	2.16514	0.051

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.35843	1
Exp 36h	1.09849	1
Exp 60h	1.82225	0.227

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.9728	1
Var 0h	0.98049	1
Var 12h I row2-row1	0.74414	0.418
Var 12h NI row2-row1	1.68425	0.34
Var 36h I row2-row1	1.36697	0.489
Var 36h NI row2-row1	0.47954	0.478
Var 60h I row2-row1	0.84084	0.582
Var 60h NI row2-row1	0.8393	0.866
Time course 0hI-0hNI	1.27121	0.603
Time course 12hI-12hNI	1.15275	0.493
Time course 36hI-36hNI	4.65546	0.004
Time course 60hI-60hNI	18.2354	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.34204	0.246
transgenic ySAMdc/azygous control (breaker)	0.64566	0.251
transgenic ySAMdc/azygous control (red)	1.06488	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81416	0.172

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71169	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.0046	1
Manapal/WT (break)	0.3763	0.333
Manapal/WT (red)	0.51446	0.315