Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.11.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76813	0.162
27DAP/17DAP	0.97768	0.957
39DAP/27DAP	1.4298	0.272
41DAP/39DAP	0.66542	0.122
42DAP/41DAP	0.96552	1
43DAP/42DAP	1.06329	1
47DAP/43DAP	0.63282	0.079
52DAP/47DAP	1.01285	0.971
57DAP/52DAP	1.40679	0.688

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0197	0.928
17DAP/reference	1.06802	0.239
27DAP/reference	0.95114	0.484
39DAP/reference	0.99354	0.885
41DAP/reference	1.11816	0.393
42DAP/reference	0.92715	0.107
43DAP/reference	1.00574	0.904
47DAP/reference	1.11892	0.085
52DAP/reference	0.9407	0.3
57DAP/reference	0.84793	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79116	0.046
27DAP/17DAP	1.1142	0.671
39DAP/27DAP	0.77818	0.073
41DAP/39DAP	1.14318	1
42DAP/41DAP	1.10208	0.836
43DAP/42DAP	0.8848	0.089
47DAP/43DAP	0.93966	0.554
52DAP/47DAP	0.61837	0.041
57DAP/52DAP	0.79203	0.267
57DAP/7DAP	0.32055	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.22387	0.027
17DAP/reference	1.6149	0.011
27DAP/reference	1.40375	0.023
39DAP/reference	1.08848	0.166
41DAP/reference	1.44324	0.015
42DAP/reference	1.43843	0.016
43DAP/reference	1.14535	0.118
47DAP/reference	0.96098	0.504
52DAP/reference	1.15313	0.352
57DAP/reference	0.94155	0.302

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13828	0.226
17DAP/reference	1.07639	0.496
27DAP/reference	1.03644	0.735
39DAP/reference	0.93487	0.298
41DAP/reference	0.87611	0.087
42DAP/reference	0.95857	0.433
43DAP/reference	1.06231	0.761
47DAP/reference	1.04234	0.603
52DAP/reference	0.93319	0.203
57DAP/reference	1.18395	0.025

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.7697	0.017
17DAP/reference	1.27523	0.371
27DAP/reference	1.36992	0.022
39DAP/reference	1.28622	0.028
41DAP/reference	1.04828	0.369
42DAP/reference	0.99036	0.816
43DAP/reference	0.87298	0.098
47DAP/reference	0.96878	0.434
52DAP/reference	0.97088	0.637
57DAP/reference	0.67205	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	3.11396	0.966
26DAP/20DAP	1.51143	0.102
34DAP/26DAP	0.761	0.142
51DAP/34DAP	1.03815	0.936
52DAP/51DAP	0.95943	1
53DAP/52DAP	1.32825	0.196
55DAP/53DAP	1.23672	0.722
57DAP/55DAP	1.15166	0.87
62DAP/57DAP	1.03258	1
68DAP/62DAP	1.02029	0.787
68DAP/14DAP	0.81938	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.3333	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85507	0.329
Mature Green Tomato/Ripe Tomato	2.46949	0.017
Immature Eggplant/Mature Eggplant	1.22785	0.051
Ripe Pepper/Ripe Tomato	0.9007	1
Mature Eggplant/Ripe Tomato	0.91442	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.08201	0.877
1-1-2/M82	1.03502	1
12-2/M82	0.85287	0.955
12-4/M82	1.14026	1
1-3/M82	1.34698	0.277
2-1-1/M82	1.11319	0.764
2-1/M82	1.16324	0.345
2-6/M82	1.09488	0.594
3-2/M82	1.06807	0.463
4-1-1/M82	1.20288	0.998
4-1/M82	1.64424	1
4-3-2/M82	1.73821	0.262
4-3/M82	1.48045	1
5-3/M82	1.34744	0.496
6-2/M82	1.47062
6-3/M82	0.95426	1
7-1/M82	1.0048	1
7-2/M82	1.12707
9-3-2/M82	1.42368	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05058
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96376
IL12-4/WTpooled	0.98689	1
IL1-4/WTpooled	1.54169
WT/WTpooled	0.93651	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	1.15339	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10763	0.823
DC3000/delta hrp 6h	0.93058	0.95
DC3000/delta hrp 12h	1.06563	1
DC3000/delta hrp 24h	1.14098	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.28818	0.043
DC3000 delta B/DC3000 delta AB	1.38782	0.13

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99323	1
Exp 36h	1.16123	0.693
Exp 60h	1.23695	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04069	1
Var 0h	0.97121	1
Var 12h I row2-row1	0.91069	0.467
Var 12h NI row2-row1	1.03296	1
Var 36h I row2-row1	1.16041	0.368
Var 36h NI row2-row1	0.91999	0.584
Var 60h I row2-row1	0.84029	0.285
Var 60h NI row2-row1	0.86424	0.69
Time course 0hI-0hNI	1.12354	0.537
Time course 12hI-12hNI	1.0415	0.738
Time course 36hI-36hNI	1.26564	0.056
Time course 60hI-60hNI	1.66738	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)	0.93206	0.33
transgenic ySAMdc/azygous control (breaker)	1.21984	1
transgenic ySAMdc/azygous control (red)	1.10245	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98178	0.5

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86021	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93098	1
Manapal/WT (break)	0.80129	0.333
Manapal/WT (red)	0.9158	0.424