Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.10.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43871	0.138
27DAP/17DAP	1.01634	1
39DAP/27DAP	1.20717	0.858
41DAP/39DAP	1.08586	0.722
42DAP/41DAP	1.58878	0.485
43DAP/42DAP	0.82482	0.767
47DAP/43DAP	1.13031	0.825
52DAP/47DAP	1.18583	0.645
57DAP/52DAP	0.91549	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01852	1
17DAP/reference	1.16134	0.028
27DAP/reference	0.97265	0.642
39DAP/reference	1.10375	0.229
41DAP/reference	1.14793	0.085
42DAP/reference	0.8999	0.025
43DAP/reference	1.07991	0.471
47DAP/reference	0.92381	0.106
52DAP/reference	0.81754	0.128
57DAP/reference	0.7202	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24453	0.094
27DAP/17DAP	1.08291	1
39DAP/27DAP	1.22329	0.478
41DAP/39DAP	0.94493	0.849
42DAP/41DAP	1.10624	0.81
43DAP/42DAP	1.14338	0.103
47DAP/43DAP	0.89062	0.28
52DAP/47DAP	1.48498	0.21
57DAP/52DAP	1.56817	0.138
57DAP/7DAP	1.01095	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03935	1
17DAP/reference	1.09627	0.244
27DAP/reference	0.94727	0.283
39DAP/reference	0.64642	0.126
41DAP/reference	0.93418	0.326
42DAP/reference	0.88618	0.2
43DAP/reference	0.79765	0.046
47DAP/reference	0.75324	0.079
52DAP/reference	0.91465	0.179
57DAP/reference	0.93992	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99204	0.831
17DAP/reference	1.07044	0.25
27DAP/reference	0.82965	0.173
39DAP/reference	0.85391	0.093
41DAP/reference	0.99812	0.683
42DAP/reference	0.98822	0.594
43DAP/reference	1.38986	0.035
47DAP/reference	1.12131	0.498
52DAP/reference	1.09685	0.194
57DAP/reference	1.30063	0.022

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87447	0.135
17DAP/reference	1.10122	0.39
27DAP/reference	0.95017	0.516
39DAP/reference	0.86016	0.092
41DAP/reference	0.93733	0.148
42DAP/reference	0.83503	0.134
43DAP/reference	1.09511	0.608
47DAP/reference	0.93838	0.357
52DAP/reference	1.01279	0.8
57DAP/reference	0.78819	0.092

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.42291	0.966
26DAP/20DAP	1.05842	0.905
34DAP/26DAP	1.2221	1
51DAP/34DAP	1.18338	0.281
52DAP/51DAP	1.21199	0.295
53DAP/52DAP	0.76965	0.101
55DAP/53DAP	1.21832	0.468
57DAP/55DAP	0.84136	0.703
62DAP/57DAP	1.46793	0.015
68DAP/62DAP	1.52525	0.936
68DAP/14DAP	0.83865	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20456	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.45595	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.12485	0.224
Mature Eggplant/Ripe Tomato	1.23572	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.15558	0.742
1-1-2/M82	0.82954	1
12-2/M82	N/A	N/A
12-4/M82	1.32789	1
1-3/M82	0.61541
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.03997	1
3-2/M82	1.06117	0.549
4-1-1/M82	N/A	N/A
4-1/M82	1.36124
4-3-2/M82	N/A	N/A
4-3/M82	1.27486	0.268
5-3/M82	0.88458	0.642
6-2/M82	N/A	N/A
6-3/M82	1.23435	1
7-1/M82	0.79055
7-2/M82	0.97158	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08909	0.277
IL2-6/WTpooled	1.12526	0.659
IL7-5/WTpooled	0.75191	1
IL7-3/WTpooled	1.06662	1
IL12-4/WTpooled	0.80875	0.71
IL1-4/WTpooled	0.92313	0.834
WT/WTpooled	1.03868	0.874

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	1.0906	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97234	1
DC3000/delta hrp 6h	1.02945	1
DC3000/delta hrp 12h	1.43481	1
DC3000/delta hrp 24h	1.64165	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.65296	0.408
DC3000 delta B/DC3000 delta AB	1.16751	0.571

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94221	1
Exp 36h	2.38696	1
Exp 60h	1.37475	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01587	1
Var 0h	0.97911	1
Var 12h I row2-row1	1.21955	0.506
Var 12h NI row2-row1	0.90715	0.488
Var 36h I row2-row1	0.98513	1
Var 36h NI row2-row1	2.43589	1
Var 60h I row2-row1	1.00133	1
Var 60h NI row2-row1	1.05671	0.904
Time course 0hI-0hNI	0.98243	0.961
Time course 12hI-12hNI	0.98724	0.931
Time course 36hI-36hNI	0.85868	0.125
Time course 60hI-60hNI	0.88982	0.026

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)	1.01091	0.921
transgenic ySAMdc/azygous control (breaker)	0.60035	0.142
transgenic ySAMdc/azygous control (red)	1.04416	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97235	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95593	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.47963	0.172
Manapal/WT (break)	0.91182	1
Manapal/WT (red)	1.15548	0.413