Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.6.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97237	0.788
27DAP/17DAP	1.12858	0.845
39DAP/27DAP	0.98642	0.782
41DAP/39DAP	1.26698	0.413
42DAP/41DAP	1.07556	0.967
43DAP/42DAP	1.15739	0.991
47DAP/43DAP	0.96239	0.815
52DAP/47DAP	1.42485	0.446
57DAP/52DAP	0.95043	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9376	0.308
17DAP/reference	1.06073	0.1
27DAP/reference	1.05531	0.314
39DAP/reference	1.02228	0.514
41DAP/reference	0.9793	0.667
42DAP/reference	0.88502	0.04
43DAP/reference	1.02872	0.838
47DAP/reference	0.98801	0.535
52DAP/reference	0.70087	0.075
57DAP/reference	0.73797	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90859	0.311
27DAP/17DAP	0.97471	0.821
39DAP/27DAP	1.05503	0.541
41DAP/39DAP	0.95192	0.875
42DAP/41DAP	0.9804	0.777
43DAP/42DAP	1.0653	0.176
47DAP/43DAP	1.00123	0.998
52DAP/47DAP	1.02788	0.915
57DAP/52DAP	1.00055	0.929
57DAP/7DAP	1.21997	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84315
17DAP/reference	0.83621	0.011
27DAP/reference	0.84593	0.01
39DAP/reference	0.8239	0.018
41DAP/reference	0.79026	0.016
42DAP/reference	0.88362	0.017
43DAP/reference	0.79749	0.011
47DAP/reference	0.8732	0.101
52DAP/reference	0.78665	0.019
57DAP/reference	0.79657	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98511	0.77
17DAP/reference	0.98485	0.611
27DAP/reference	0.88245	0.139
39DAP/reference	0.88295	0.227
41DAP/reference	0.79494	0.024
42DAP/reference	0.82525	0.05
43DAP/reference	0.98354	0.646
47DAP/reference	0.95064	0.302
52DAP/reference	0.98469	0.576
57DAP/reference	1.07602	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83311	0.249
17DAP/reference	0.95417	0.624
27DAP/reference	0.90509	0.218
39DAP/reference	0.83206	0.016
41DAP/reference	0.77505	0.148
42DAP/reference	0.76128	0.134
43DAP/reference	0.80755	0.098
47DAP/reference	0.9126	0.278
52DAP/reference	0.76729	0.086
57DAP/reference	0.44429	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01874	0.966
26DAP/20DAP	0.95726	1
34DAP/26DAP	1.07833	0.819
51DAP/34DAP	0.86907	0.164
52DAP/51DAP	1.12355	0.492
53DAP/52DAP	0.9469	0.723
55DAP/53DAP	0.97364	0.784
57DAP/55DAP	0.87238	0.506
62DAP/57DAP	1.12705	0.833
68DAP/62DAP	1.14414	0.672
68DAP/14DAP	1.00169	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2381	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.78376	0.29
Mature Green Tomato/Ripe Tomato	1.59331	0.237
Immature Eggplant/Mature Eggplant	4.61306	0.05
Ripe Pepper/Ripe Tomato	3.05585	1
Mature Eggplant/Ripe Tomato	1.08595	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92699	0.944
1-1-2/M82	1.02212	1
12-2/M82	1.07048	1
12-4/M82	0.95811	1
1-3/M82	0.90567	0.441
2-1-1/M82	1.1704	0.457
2-1/M82	0.95289	0.519
2-6/M82	0.93952	1
3-2/M82	0.91703	0.752
4-1-1/M82	1.01293	1
4-1/M82	0.84224	1
4-3-2/M82	0.80532	0.698
4-3/M82	0.69735	0.611
5-3/M82	0.86552	0.642
6-2/M82	0.93278
6-3/M82	1.07153	1
7-1/M82	0.93922	0.466
7-2/M82	0.99553	1
9-3-2/M82	0.95425	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.19011	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.31817	0.362
IL12-4/WTpooled	1.24375	0.553
IL1-4/WTpooled	0.65252
WT/WTpooled	0.97985	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	1.03623	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94363	1
DC3000/delta hrp 6h	0.82805	0.95
DC3000/delta hrp 12h	1.03091	1
DC3000/delta hrp 24h	0.90408	0.22

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99945	1
DC3000 delta B/DC3000 delta AB	1.03835	0.646

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11643	1
Exp 36h	1.40742	1
Exp 60h	1.16491	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01292	1
Var 0h	0.86772	0.196
Var 12h I row2-row1	1.14658	0.296
Var 12h NI row2-row1	1.00856	1
Var 36h I row2-row1	1.07137	1
Var 36h NI row2-row1	0.91274	0.584
Var 60h I row2-row1	1.27097	0.562
Var 60h NI row2-row1	1.25197	0.904
Time course 0hI-0hNI	1.14542	0.603
Time course 12hI-12hNI	1.0088	1
Time course 36hI-36hNI	0.90027	0.039
Time course 60hI-60hNI	1.02673	1

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)	0.80151	0.246
transgenic ySAMdc/azygous control (breaker)	1.03041	1
transgenic ySAMdc/azygous control (red)	1.03552	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05483	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23334	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.60286	1
Manapal/WT (break)	0.56558	0.333
Manapal/WT (red)	0.74605	0.216