Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.17.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95721	0.689
27DAP/17DAP	0.96341	0.908
39DAP/27DAP	1.29888	0.658
41DAP/39DAP	0.77378	0.235
42DAP/41DAP	0.82657	1
43DAP/42DAP	1.2314	0.854
47DAP/43DAP	0.65487	0.113
52DAP/47DAP	0.97943	0.789
57DAP/52DAP	1.17044	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11708	0.366
17DAP/reference	1.30282	0.166
27DAP/reference	1.12849	0.161
39DAP/reference	1.30969	0.028
41DAP/reference	1.20065	0.221
42DAP/reference	1.19644	0.065
43DAP/reference	1.11727	0.325
47DAP/reference	1.2441	0.022
52DAP/reference	1.25436	0.128
57DAP/reference	1.06999	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79004	0.048
27DAP/17DAP	1.06966	0.863
39DAP/27DAP	0.86819	0.243
41DAP/39DAP	1.01723	0.98
42DAP/41DAP	1.0741	0.886
43DAP/42DAP	0.89947	0.149
47DAP/43DAP	0.94062	0.597
52DAP/47DAP	0.60923	0.05
57DAP/52DAP	0.95823	0.646
57DAP/7DAP	0.36771	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85462	0.104
17DAP/reference	1.108	0.822
27DAP/reference	1.17757	0.06
39DAP/reference	0.98962	0.64
41DAP/reference	1.00198	0.677
42DAP/reference	1.00092	0.791
43DAP/reference	0.97565	0.385
47DAP/reference	1.21855	0.254
52DAP/reference	0.77743	0.097
57DAP/reference	0.98601	0.549

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93721	0.592
17DAP/reference	0.9381	0.693
27DAP/reference	1.37304	0.104
39DAP/reference	1.1426	1
41DAP/reference	1.28021	0.094
42DAP/reference	1.24317	0.031
43DAP/reference	1.03955	1
47DAP/reference	1.1074	0.218
52DAP/reference	1.22315	0.065
57DAP/reference	1.14402	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86749	0.23
17DAP/reference	0.91409	0.313
27DAP/reference	1.04008	1
39DAP/reference	1.03131	0.987
41DAP/reference	1.16417	0.296
42DAP/reference	1.20409	0.076
43DAP/reference	1.22228	0.241
47DAP/reference	1.12249	0.68
52DAP/reference	1.15669	0.473
57DAP/reference	1.32589	0.067

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10155	0.207
26DAP/20DAP	1.9069	0.106
34DAP/26DAP	0.769	0.18
51DAP/34DAP	1.15502	0.814
52DAP/51DAP	1.1176	0.579
53DAP/52DAP	1.0222	0.99
55DAP/53DAP	0.72017	0.404
57DAP/55DAP	1.06515	1
62DAP/57DAP	2.25531	0.767
68DAP/62DAP	1.39516	0.285
68DAP/14DAP	1.47767	0.636

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.41893	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	2.33801	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.51831
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.2963	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	1.46898	0.508
4-3/M82	0.6672
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.72768
9-3-2/M82	1.12864

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79406	0.243
IL2-6/WTpooled	0.95001	1
IL7-5/WTpooled	0.58896	1
IL7-3/WTpooled	1.14019	1
IL12-4/WTpooled	1.0737	0.553
IL1-4/WTpooled	0.85738	0.699
WT/WTpooled	1.07801	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	1.01439	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98881	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	44.9026	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.3482	0.046
DC3000 delta B/DC3000 delta AB	1.40463	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96715	1
Var 0h	0.5312	0.936
Var 12h I row2-row1	0.93982	0.705
Var 12h NI row2-row1	1.10584	0.649
Var 36h I row2-row1	1.20194	0.298
Var 36h NI row2-row1	0.9101	0.61
Var 60h I row2-row1	0.77938	0.293
Var 60h NI row2-row1	0.8383	0.756
Time course 0hI-0hNI	1.1195	0.574
Time course 12hI-12hNI	0.98897	0.956
Time course 36hI-36hNI	1.22543	0.009
Time course 60hI-60hNI	1.56127	0.009

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)	26.4569	0.699
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.75208	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.59433	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.32823	0.164