Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.10.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.74909	0.272
27DAP/17DAP	3.05027	0.066
39DAP/27DAP	1.86998	0.04
41DAP/39DAP	0.5341	0.042
42DAP/41DAP	1.0282	1
43DAP/42DAP	3.17756	0.018
47DAP/43DAP	0.99983	0.953
52DAP/47DAP	0.90508	0.702
57DAP/52DAP	0.91678	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79406	0.046
17DAP/reference	0.9565	0.419
27DAP/reference	1.38878	0.012
39DAP/reference	1.36074	0.07
41DAP/reference	1.21175	0.133
42DAP/reference	2.32387	0.001
43DAP/reference	1.48418	0.007
47DAP/reference	2.73173	0.001
52DAP/reference	1.67648	0.019
57DAP/reference	1.43197	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.41428	0.172
27DAP/17DAP	1.45867	0.045
39DAP/27DAP	1.6748	0.054
41DAP/39DAP	0.60261	0.028
42DAP/41DAP	1.20494	0.139
43DAP/42DAP	2.49067	0.013
47DAP/43DAP	0.96557	0.846
52DAP/47DAP	1.18619	0.517
57DAP/52DAP	1.71099	0.036
57DAP/7DAP	5.3049	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83722	0.168
17DAP/reference	1.16723	0.162
27DAP/reference	1.27993	0.01
39DAP/reference	1.16795	0.157
41DAP/reference	1.34163	0.015
42DAP/reference	1.37744	0.059
43DAP/reference	1.77245	0.008
47DAP/reference	1.50548	0.022
52DAP/reference	1.41348	0.007
57DAP/reference	1.28318	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81415	0.062
17DAP/reference	1.21646	0.038
27DAP/reference	1.12424	0.16
39DAP/reference	0.95653	0.227
41DAP/reference	1.09367	0.642
42DAP/reference	1.27187	0.024
43DAP/reference	0.91225	0.298
47DAP/reference	0.92261	0.044
52DAP/reference	1.09623	0.098
57DAP/reference	0.9269	0.125

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90759	0.23
17DAP/reference	0.91767	0.417
27DAP/reference	1.22547	0.026
39DAP/reference	1.12203	0.084
41DAP/reference	1.02916	0.84
42DAP/reference	1.20502	0.142
43DAP/reference	1.55511	0.006
47DAP/reference	2.53197	0.005
52DAP/reference	1.94594	0.028
57DAP/reference	2.06469	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.74539	0.733
26DAP/20DAP	1.02295	1
34DAP/26DAP	0.97737	0.972
51DAP/34DAP	1.41562	0.171
52DAP/51DAP	0.92113	1
53DAP/52DAP	0.9562	0.876
55DAP/53DAP	1.15598	0.79
57DAP/55DAP	1.03339	0.859
62DAP/57DAP	1.00243	1
68DAP/62DAP	0.511	0.059
68DAP/14DAP	0.83225	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.98793	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.22263	0.091
Mature Green Tomato/Ripe Tomato	0.33972	0.038
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.1289	0.224
Mature Eggplant/Ripe Tomato	0.159	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.59046
1-1-2/M82	1.24459	1
12-2/M82	0.76881	0.862
12-4/M82	1.15614	1
1-3/M82	N/A	N/A
2-1-1/M82	0.95935
2-1/M82	0.76308
2-6/M82	0.97975
3-2/M82	0.97461	1
4-1-1/M82	1.11107	1
4-1/M82	N/A	N/A
4-3-2/M82	1.14376	1
4-3/M82	0.99777	1
5-3/M82	1.08594	1
6-2/M82	0.65292	0.481
6-3/M82	0.95343	1
7-1/M82	0.90302	0.509
7-2/M82	1.8014	0.302
9-3-2/M82	1.35975	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.09742	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87532	1
IL12-4/WTpooled	1.00392	1
IL1-4/WTpooled	1.71506	0.426
WT/WTpooled	1.09547	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	0.8284	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98455	1
DC3000/delta hrp 6h	0.98059	0.95
DC3000/delta hrp 12h	1.03134	1
DC3000/delta hrp 24h	1.40573	0.067

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94919	0.955
DC3000 delta B/DC3000 delta AB	0.81448	0.142

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92417	1
Exp 36h	0.76845	0.749
Exp 60h	0.67716	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99666	1
Var 0h	1.0217	0.98
Var 12h I row2-row1	0.94159	0.705
Var 12h NI row2-row1	1.08972	0.649
Var 36h I row2-row1	0.80005	1
Var 36h NI row2-row1	1.45339	0.482
Var 60h I row2-row1	1.07734	1
Var 60h NI row2-row1	1.36381	0.904
Time course 0hI-0hNI	0.99481	0.991
Time course 12hI-12hNI	0.92496	0.287
Time course 36hI-36hNI	0.75475	0.023
Time course 60hI-60hNI	0.26295	0.006

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)	1.15975	0.268
transgenic ySAMdc/azygous control (breaker)	1.1607	0.172
transgenic ySAMdc/azygous control (red)	1.00607	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.25764	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06936	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32053	0.307
Manapal/WT (break)	1.09138	1
Manapal/WT (red)	1.05693	1