Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.11.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8668	0.496
27DAP/17DAP	0.99425	1
39DAP/27DAP	1.43203	0.229
41DAP/39DAP	1.25783	0.758
42DAP/41DAP	1.04402	1
43DAP/42DAP	0.90369	0.713
47DAP/43DAP	1.03217	0.98
52DAP/47DAP	1.22757	0.639
57DAP/52DAP	0.86148	0.79

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90673	0.145
17DAP/reference	0.96291	0.503
27DAP/reference	1.04321	0.58
39DAP/reference	0.93158	0.261
41DAP/reference	0.92989	0.341
42DAP/reference	0.89223	0.054
43DAP/reference	0.97025	0.631
47DAP/reference	0.96155	0.345
52DAP/reference	0.91102	0.073
57DAP/reference	0.94776	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32886	0.129
27DAP/17DAP	1.01203	0.969
39DAP/27DAP	1.02	1
41DAP/39DAP	1.09077	0.921
42DAP/41DAP	0.9632	0.712
43DAP/42DAP	1.09603	0.413
47DAP/43DAP	0.99067	0.971
52DAP/47DAP	0.96497	0.868
57DAP/52DAP	1.20033	0.202
57DAP/7DAP	2.20759	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95382	0.445
17DAP/reference	1.08207	0.477
27DAP/reference	1.04873	0.551
39DAP/reference	1.26417	0.222
41DAP/reference	1.14044	0.445
42DAP/reference	1.18407	0.308
43DAP/reference	1.15507	0.603
47DAP/reference	1.04336	0.549
52DAP/reference	1.04164	1
57DAP/reference	1.0026	0.748

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17713	0.124
17DAP/reference	1.11198	0.147
27DAP/reference	1.05156	0.607
39DAP/reference	1.00202	0.702
41DAP/reference	1.0292	0.862
42DAP/reference	1.06432	0.621
43DAP/reference	1.34551	0.056
47DAP/reference	1.06435	0.343
52DAP/reference	1.01368	0.761
57DAP/reference	1.0602	0.508

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91853	0.197
17DAP/reference	1.07663	0.833
27DAP/reference	1.21021	0.171
39DAP/reference	1.13246	0.163
41DAP/reference	1.16497	0.257
42DAP/reference	1.0308	0.848
43DAP/reference	0.80988	0.064
47DAP/reference	0.92487	0.306
52DAP/reference	1.41274	0.558
57DAP/reference	1.14157	0.873

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.39589	0.966
26DAP/20DAP	1.12262	1
34DAP/26DAP	0.97596	1
51DAP/34DAP	1.0948	0.949
52DAP/51DAP	1.01263	0.965
53DAP/52DAP	1.11487	0.83
55DAP/53DAP	0.98823	0.886
57DAP/55DAP	1.24325	0.728
62DAP/57DAP	0.72784	0.466
68DAP/62DAP	1.43464	0.821
68DAP/14DAP	0.84244	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09718	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.07673	1
Mature Green Tomato/Ripe Tomato	0.74659	0.256
Immature Eggplant/Mature Eggplant	1.01911	1
Ripe Pepper/Ripe Tomato	1.09372	1
Mature Eggplant/Ripe Tomato	1.30932	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03613	1
1-1-2/M82	1.05773	1
12-2/M82	N/A	N/A
12-4/M82	1.17424
1-3/M82	0.8388
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	1.21942
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.91053	1
6-2/M82	N/A	N/A
6-3/M82	1.07674
7-1/M82	0.88295
7-2/M82	0.85226	0.881
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.00066	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.26494	1
IL12-4/WTpooled	1.11854	0.595
IL1-4/WTpooled	1.00618	1
WT/WTpooled	1.04437	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	0.92112	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09051	0.671
DC3000/delta hrp 6h	1.01227	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.00734	0.84

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	1.02261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00517	1
Exp 36h	0.86921	0.589
Exp 60h	0.96295	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.13978	1
Var 0h	0.9631	1
Var 12h I row2-row1	1.02289	0.736
Var 12h NI row2-row1	0.95053	0.713
Var 36h I row2-row1	1.1236	1
Var 36h NI row2-row1	0.7595	0.549
Var 60h I row2-row1	0.9206	0.832
Var 60h NI row2-row1	1.00652	1
Time course 0hI-0hNI	0.9624	0.711
Time course 12hI-12hNI	0.97722	0.742
Time course 36hI-36hNI	1.06788	0.218
Time course 60hI-60hNI	1.29762	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)	1.10757	0.326
transgenic ySAMdc/azygous control (breaker)	0.9172	0.49
transgenic ySAMdc/azygous control (red)	0.89334	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98363	0.242

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84766	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99183	1
Manapal/WT (break)	1.17701	0.381
Manapal/WT (red)	1.13461	1