Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.3.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09089	0.827
27DAP/17DAP	1.06628	1
39DAP/27DAP	1.3301	0.429
41DAP/39DAP	0.84619	0.412
42DAP/41DAP	0.94101	1
43DAP/42DAP	0.8876	0.708
47DAP/43DAP	0.9132	0.696
52DAP/47DAP	0.80665	0.554
57DAP/52DAP	1.48135	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09527	0.567
17DAP/reference	1.11541	0.096
27DAP/reference	0.85955	0.157
39DAP/reference	1.06493	0.691
41DAP/reference	1.33348	0.013
42DAP/reference	1.09302	1
43DAP/reference	1.09758
47DAP/reference	1.14029	0.478
52DAP/reference	0.87335	0.25
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05879	0.569
27DAP/17DAP	1.10723	0.69
39DAP/27DAP	0.81675	0.132
41DAP/39DAP	1.13553	0.469
42DAP/41DAP	1.02178	0.91
43DAP/42DAP	0.91131	0.431
47DAP/43DAP	1.07781	0.812
52DAP/47DAP	0.92293	0.575
57DAP/52DAP	1.08321	0.793
57DAP/7DAP	1.06224	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70982	0.06
17DAP/reference	0.65396	0.012
27DAP/reference	0.85852	0.048
39DAP/reference	0.6614	0.012
41DAP/reference	0.6206	0.023
42DAP/reference	0.67553	0.012
43DAP/reference	0.62379	0.01
47DAP/reference	0.75404	0.057
52DAP/reference	0.57978	0.012
57DAP/reference	0.96555	0.215

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38743	0.234
17DAP/reference	1.19202	0.385
27DAP/reference	1.20183	0.163
39DAP/reference	1.1189	0.686
41DAP/reference	0.92073	0.348
42DAP/reference	1.11346	0.519
43DAP/reference	1.53336	0.062
47DAP/reference	0.9077	0.092
52DAP/reference	1.33969	0.041
57DAP/reference	1.25115	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86334	0.158
17DAP/reference	1.02746	0.87
27DAP/reference	0.71958	0.033
39DAP/reference	0.8412	0.058
41DAP/reference	0.84707	0.119
42DAP/reference	0.97881	0.671
43DAP/reference	0.96703	0.484
47DAP/reference	1.08109	0.76
52DAP/reference	0.7876	0.155
57DAP/reference	1.01864	0.693

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.44762	0.817
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.036	1
51DAP/34DAP	0.94411	0.747
52DAP/51DAP	N/A	N/A
53DAP/52DAP	0.85554	0.484
55DAP/53DAP	1.12436	0.813
57DAP/55DAP	0.99009	0.944
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.02082	1
68DAP/14DAP	1.44081	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.37471	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	1.3098	0.209
Immature Eggplant/Mature Eggplant	1.43668
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.53378

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09844	0.591
1-1-2/M82	0.75369
12-2/M82	N/A	N/A
12-4/M82	1.01044	1
1-3/M82	0.62113
2-1-1/M82	1.23364	0.26
2-1/M82	N/A	N/A
2-6/M82	0.90599	1
3-2/M82	N/A	N/A
4-1-1/M82	0.8602	0.883
4-1/M82	1.28067
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.83188	0.642
6-2/M82	0.7022
6-3/M82	0.96841	0.587
7-1/M82	N/A	N/A
7-2/M82	0.7548	0.565
9-3-2/M82	0.96004	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81075	0.247
IL2-6/WTpooled	1.32562
IL7-5/WTpooled	0.92565	1
IL7-3/WTpooled	0.9226
IL12-4/WTpooled	0.93916
IL1-4/WTpooled	0.92145	0.699
WT/WTpooled	0.7609

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	1.35664	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09857	0.894
DC3000/delta hrp 6h	0.94323	0.95
DC3000/delta hrp 12h	1.07039	1
DC3000/delta hrp 24h	0.90243	0.28

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99127	1
DC3000 delta B/DC3000 delta AB	1.14002	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12098	1
Exp 36h	1.18951	0.693
Exp 60h	1.18791	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03272	1
Var 0h	0.71111	1
Var 12h I row2-row1	0.92522	0.77
Var 12h NI row2-row1	1.36461	0.165
Var 36h I row2-row1	0.98501	1
Var 36h NI row2-row1	1.00278	1
Var 60h I row2-row1	0.8247	0.374
Var 60h NI row2-row1	0.95081	1
Time course 0hI-0hNI	0.98068	0.942
Time course 12hI-12hNI	0.94269	0.515
Time course 36hI-36hNI	1.32085	0.009
Time course 60hI-60hNI	2.0128	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)	1.1059	0.286
transgenic ySAMdc/azygous control (breaker)	0.89198	0.142
transgenic ySAMdc/azygous control (red)	0.88357	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9751	0.16

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66895	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.27958	0.09
Manapal/WT (break)	1.20082	0.381
Manapal/WT (red)	1.05455	1