Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69528	0.105
27DAP/17DAP	0.83358	0.553
39DAP/27DAP	3.94952	0.02
41DAP/39DAP	1.09909	0.982
42DAP/41DAP	0.66356	0.774
43DAP/42DAP	0.76913	0.664
47DAP/43DAP	0.33504	0.046
52DAP/47DAP	3.76353	0.041
57DAP/52DAP	0.65483	0.507

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25972	0.078
17DAP/reference	1.04299	0.193
27DAP/reference	1.01707	0.637
39DAP/reference	0.98563	0.762
41DAP/reference	1.03622	0.48
42DAP/reference	0.98917	0.315
43DAP/reference	0.97054	0.48
47DAP/reference	0.98431	0.418
52DAP/reference	0.96469	0.427
57DAP/reference	0.89148	0.029

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.1589	0.024
27DAP/17DAP	1.41879	0.079
39DAP/27DAP	0.93574	0.622
41DAP/39DAP	1.96622	0.08
42DAP/41DAP	1.05722	0.757
43DAP/42DAP	5.79184	0.013
47DAP/43DAP	1.30508	0.094
52DAP/47DAP	0.40902	0.108
57DAP/52DAP	9.41456	0.029
57DAP/7DAP	1.15771	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99719	0.682
17DAP/reference	0.87985	0.028
27DAP/reference	0.84631	0.01
39DAP/reference	0.91227	0.017
41DAP/reference	0.94461	0.311
42DAP/reference	0.9296	0.032
43DAP/reference	0.90028	0.011
47DAP/reference	1.21442	0.266
52DAP/reference	0.91226	0.083
57DAP/reference	0.89555	0.032

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17881	0.049
17DAP/reference	1.01555	0.839
27DAP/reference	1.02258	0.888
39DAP/reference	1.18819	0.175
41DAP/reference	1.01837	1
42DAP/reference	1.07898	0.543
43DAP/reference	1.06525	0.453
47DAP/reference	1.00519	1
52DAP/reference	1.00308	1
57DAP/reference	1.00388	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92037	0.214
17DAP/reference	0.99412	0.825
27DAP/reference	0.90184	0.052
39DAP/reference	0.91915	0.246
41DAP/reference	0.88545	0.05
42DAP/reference	0.76228	0.071
43DAP/reference	0.97565	0.545
47DAP/reference	1.0029	1
52DAP/reference	0.93462	0.582
57DAP/reference	0.77611	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05158	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.78699	0.294
51DAP/34DAP	0.80745	0.472
52DAP/51DAP	0.96542	1
53DAP/52DAP	1.88612	0.077
55DAP/53DAP	0.83416	0.163
57DAP/55DAP	0.94776	0.783
62DAP/57DAP	0.76801	0.28
68DAP/62DAP	1.01703	0.971
68DAP/14DAP	0.93227	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.97396	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89936
Mature Green Tomato/Ripe Tomato	0.15754	0.016
Immature Eggplant/Mature Eggplant	1.38864	0.05
Ripe Pepper/Ripe Tomato	0.17814	0.224
Mature Eggplant/Ripe Tomato	0.15738	0.234

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	0.94367
12-4/M82	0.78591	0.272
1-3/M82	8.35661	0.248
2-1-1/M82	0.67208
2-1/M82	N/A	N/A
2-6/M82	0.68062
3-2/M82	2.14234
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.0906
4-3/M82	0.28606
5-3/M82	1.04229	1
6-2/M82	9.37453
6-3/M82	N/A	N/A
7-1/M82	4.43159
7-2/M82	2.30715
9-3-2/M82	0.91852

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.36742	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.65212
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.29342	0.426
WT/WTpooled	0.82633	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	2.28007

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.68969	0.642
DC3000/delta hrp 6h	0.89644	0.95
DC3000/delta hrp 12h	0.96254	1
DC3000/delta hrp 24h	0.87696	0.22

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00555	1
Exp 36h	1.53964	1
Exp 60h	0.9254	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.90453
Var 0h	1.03919	0.98
Var 12h I row2-row1	0.98976	1
Var 12h NI row2-row1	0.75754	0.627
Var 36h I row2-row1	1.68639	0.908
Var 36h NI row2-row1	1.58495
Var 60h I row2-row1	1.30151
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.11237	0.833
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	1.91988	0.401
Time course 60hI-60hNI	4.30267	0.359

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)	1.96636	0.212
transgenic ySAMdc/azygous control (breaker)	0.94974	1
transgenic ySAMdc/azygous control (red)	1.0669	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07843	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8354	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01762	1
Manapal/WT (break)	0.86519	1
Manapal/WT (red)	0.57667	0.229