Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.8.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90704	0.381
27DAP/17DAP	0.9831	1
39DAP/27DAP	1.24038	0.38
41DAP/39DAP	1.23391	0.372
42DAP/41DAP	1.28268	0.276
43DAP/42DAP	1.19888	0.816
47DAP/43DAP	1.05562	0.889
52DAP/47DAP	0.9784	0.851
57DAP/52DAP	1.47571	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76121	0.071
17DAP/reference	0.84868	0.015
27DAP/reference	0.96958	0.654
39DAP/reference	0.92301	0.412
41DAP/reference	0.89523	0.267
42DAP/reference	0.75466	0.062
43DAP/reference	0.85505	0.41
47DAP/reference	0.80188	0.013
52DAP/reference	1.02683	0.768
57DAP/reference	1.29748	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.4739	0.02
27DAP/17DAP	1.33707	0.073
39DAP/27DAP	0.79751	0.054
41DAP/39DAP	0.83174	0.42
42DAP/41DAP	1.10057	0.727
43DAP/42DAP	1.07291	0.25
47DAP/43DAP	0.93516	0.457
52DAP/47DAP	1.01966	0.982
57DAP/52DAP	0.90274	0.507
57DAP/7DAP	0.48121	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11756	0.491
17DAP/reference	1.06975	0.688
27DAP/reference	0.95019	0.325
39DAP/reference	0.86653	0.109
41DAP/reference	0.81759	0.082
42DAP/reference	1.11863	0.308
43DAP/reference	1.33097	0.037
47DAP/reference	1.00976	1
52DAP/reference	1.06133	0.563
57DAP/reference	1.08051	0.654

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14949	0.501
17DAP/reference	1.08334	0.961
27DAP/reference	0.80226	0.108
39DAP/reference	0.96085	0.428
41DAP/reference	1.0092	0.631
42DAP/reference	0.93028	0.355
43DAP/reference	0.97761	0.633
47DAP/reference	1.11905	0.232
52DAP/reference	0.62267	0.009
57DAP/reference	0.92829	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03619	0.644
17DAP/reference	0.97333	0.636
27DAP/reference	1.00239	0.883
39DAP/reference	0.97415	0.544
41DAP/reference	0.90055	0.293
42DAP/reference	0.91543	0.22
43DAP/reference	1.01487	0.894
47DAP/reference	0.73254	0.191
52DAP/reference	0.80638	0.238
57DAP/reference	1.01565	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14422	0.966
26DAP/20DAP	0.84797	1
34DAP/26DAP	0.9748	0.972
51DAP/34DAP	0.9163	0.587
52DAP/51DAP	1.11919	0.542
53DAP/52DAP	0.72265	0.254
55DAP/53DAP	0.63375	0.017
57DAP/55DAP	1.00734	0.921
62DAP/57DAP	0.70434	0.466
68DAP/62DAP	1.05329	0.956
68DAP/14DAP	1.01758	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.64593	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.74569	0.377
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.17056	1
Mature Eggplant/Ripe Tomato	2.98846

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93066
12-2/M82	1.12174
12-4/M82	1.20928	1
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.7596	0.487
4-3/M82	N/A	N/A
5-3/M82	0.94487
6-2/M82	N/A	N/A
6-3/M82	0.87945	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.62668	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05712	1
IL2-6/WTpooled	1.0074	1
IL7-5/WTpooled	0.88306
IL7-3/WTpooled	1.08175	1
IL12-4/WTpooled	0.9387	1
IL1-4/WTpooled	1.12132	1
WT/WTpooled	1.10549	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	1.24059	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01982	1
DC3000/delta hrp 6h	1.50565	0.582
DC3000/delta hrp 12h	1.09752	1
DC3000/delta hrp 24h	0.65439	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47129	0.023
DC3000 delta B/DC3000 delta AB	0.55404	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16304	1
Exp 36h	1.08292	1
Exp 60h	1.14073	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99409	1
Var 0h	1.02444	1
Var 12h I row2-row1	0.86265	0.39
Var 12h NI row2-row1	0.91635	0.713
Var 36h I row2-row1	1.06984	0.41
Var 36h NI row2-row1	1.24785	0.482
Var 60h I row2-row1	0.84372	0.306
Var 60h NI row2-row1	1.0018	1
Time course 0hI-0hNI	1.22756	0.182
Time course 12hI-12hNI	0.9217	0.39
Time course 36hI-36hNI	0.9068	0.169
Time course 60hI-60hNI	0.38279	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)	1.07411	0.541
transgenic ySAMdc/azygous control (breaker)	0.60612	0.142
transgenic ySAMdc/azygous control (red)	1.00007	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00801	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91813	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.72239	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.65768	0.181