Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82729	0.253
27DAP/17DAP	0.86716	0.589
39DAP/27DAP	1.64584	0.1
41DAP/39DAP	0.69376	0.077
42DAP/41DAP	1.08825	1
43DAP/42DAP	1.30352	0.501
47DAP/43DAP	0.58631	0.057
52DAP/47DAP	2.08651	0.249
57DAP/52DAP	0.91158	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82018	0.094
17DAP/reference	0.80078	0.01
27DAP/reference	0.84927	0.109
39DAP/reference	0.7132	0.009
41DAP/reference	0.72374	0.013
42DAP/reference	0.93198	0.069
43DAP/reference	0.87965	0.18
47DAP/reference	0.96138	0.322
52DAP/reference	1.13963	0.018
57DAP/reference	1.15957	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66044	0.044
27DAP/17DAP	1.08733	0.617
39DAP/27DAP	0.94653	0.668
41DAP/39DAP	1.10508	0.781
42DAP/41DAP	1.15166	0.124
43DAP/42DAP	1.37537	0.017
47DAP/43DAP	1.04353	0.678
52DAP/47DAP	0.72641	0.088
57DAP/52DAP	1.19203	0.333
57DAP/7DAP	1.05405	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12782	0.274
17DAP/reference	1.30156	0.147
27DAP/reference	1.14114	0.371
39DAP/reference	1.06733	0.601
41DAP/reference	1.09629	0.678
42DAP/reference	1.16242	0.308
43DAP/reference	1.31239	0.014
47DAP/reference	1.19213	0.155
52DAP/reference	1.10076	0.636
57DAP/reference	1.02479	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6965	0.007
17DAP/reference	0.75892	0.01
27DAP/reference	0.95793	0.407
39DAP/reference	0.94499	0.306
41DAP/reference	0.95394	0.315
42DAP/reference	1.03882	1
43DAP/reference	0.83644	0.068
47DAP/reference	0.79142	0.01
52DAP/reference	0.7931	0.072
57DAP/reference	0.79249	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17744	0.176
17DAP/reference	1.08677	0.657
27DAP/reference	1.2552	0.198
39DAP/reference	1.11857	0.227
41DAP/reference	1.02096	1
42DAP/reference	1.15505	0.163
43DAP/reference	0.99228	0.66
47DAP/reference	0.89086	0.114
52DAP/reference	1.12527	0.212
57DAP/reference	1.07927	0.419

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98162	1
26DAP/20DAP	0.82764	0.512
34DAP/26DAP	0.69339	0.2
51DAP/34DAP	0.81174
52DAP/51DAP	0.84046	1
53DAP/52DAP	1.46945	0.07
55DAP/53DAP	0.99016	0.886
57DAP/55DAP	0.83132	0.313
62DAP/57DAP	1.86039	0.133
68DAP/62DAP	1.34836	0.22
68DAP/14DAP	1.35966	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.20237	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.49898	0.105
Mature Green Tomato/Ripe Tomato	0.44899	0.018
Immature Eggplant/Mature Eggplant	1.05373	0.633
Ripe Pepper/Ripe Tomato	1.28249	1
Mature Eggplant/Ripe Tomato	1.16908	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.76936
12-2/M82	1.13051
12-4/M82	1.01045	1
1-3/M82	1.55835
2-1-1/M82	0.73149
2-1/M82	0.83594
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	1.79736
4-3-2/M82	1.42375	0.284
4-3/M82	0.99511	1
5-3/M82	0.92989	1
6-2/M82	0.97111	1
6-3/M82	0.78663	0.982
7-1/M82	0.73824
7-2/M82	N/A	N/A
9-3-2/M82	1.09135	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.40737
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.18393
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.20269	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88244	0.849
DC3000/delta hrp 6h	0.93004	0.95
DC3000/delta hrp 12h	1.05218	1
DC3000/delta hrp 24h	0.56281	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62064	0.024
DC3000 delta B/DC3000 delta AB	0.4774	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84487	0.328
Exp 36h	0.77889	0.456
Exp 60h	0.52454	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02474	1
Var 0h	1.35507	0.374
Var 12h I row2-row1	0.8686	0.338
Var 12h NI row2-row1	0.64748	0.33
Var 36h I row2-row1	0.85971	0.805
Var 36h NI row2-row1	1.61832	1
Var 60h I row2-row1	0.90071	0.832
Var 60h NI row2-row1	1.35928	0.904
Time course 0hI-0hNI	0.71338	0.047
Time course 12hI-12hNI	1.08593	0.65
Time course 36hI-36hNI	0.95433	0.433
Time course 60hI-60hNI	0.20877	0.005

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)	0.95178	0.324
transgenic ySAMdc/azygous control (breaker)	1.04104	1
transgenic ySAMdc/azygous control (red)	1.03308	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96012	0.431

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.48681	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9525	1
Manapal/WT (break)	0.86824	0.333
Manapal/WT (red)	0.66015	0.181