Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.11.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30231	0.786
27DAP/17DAP	1.11622	0.866
39DAP/27DAP	1.61453	0.175
41DAP/39DAP	0.84115	0.403
42DAP/41DAP	0.8901	0.774
43DAP/42DAP	1.08439	0.937
47DAP/43DAP	1.85114	0.261
52DAP/47DAP	1.4265	0.307
57DAP/52DAP	1.01934	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79487	0.066
17DAP/reference	0.94344	0.536
27DAP/reference	0.8078	0.039
39DAP/reference	1.02402	0.786
41DAP/reference	0.91474	0.267
42DAP/reference	1.00623	0.665
43DAP/reference	1.5205	0.008
47DAP/reference	3.15168	0.001
52DAP/reference	2.39915	0.007
57DAP/reference	1.5053	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13237	0.241
27DAP/17DAP	0.99988	1
39DAP/27DAP	0.95277	0.622
41DAP/39DAP	1.23049	0.531
42DAP/41DAP	0.8943	0.245
43DAP/42DAP	0.80562	0.022
47DAP/43DAP	1.01676	0.934
52DAP/47DAP	1.16422	0.455
57DAP/52DAP	1.12975	0.378
57DAP/7DAP	1.06133	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00346	1
17DAP/reference	0.66272	0.011
27DAP/reference	1.33367	0.02
39DAP/reference	0.80147	0.073
41DAP/reference	1.04767	0.539
42DAP/reference	1.19829	0.174
43DAP/reference	0.96268	0.403
47DAP/reference	1.07804	0.776
52DAP/reference	0.89571	0.163
57DAP/reference	0.37893	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76114	0.021
17DAP/reference	0.69488	0.004
27DAP/reference	1.15298	0.249
39DAP/reference	1.03023	0.783
41DAP/reference	0.76631	0.027
42DAP/reference	0.97017	0.321
43DAP/reference	1.10162	0.276
47DAP/reference	0.94093	0.214
52DAP/reference	0.85142	0.066
57DAP/reference	0.94449	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81837	0.05
17DAP/reference	0.78004	0.071
27DAP/reference	0.90318	0.119
39DAP/reference	0.78596	0.018
41DAP/reference	0.82774	0.05
42DAP/reference	0.95792	0.445
43DAP/reference	0.88896	0.171
47DAP/reference	2.39364	0.006
52DAP/reference	1.97389	0.03
57DAP/reference	2.3181	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01307	1
26DAP/20DAP	1.27456	0.369
34DAP/26DAP	0.88543	0.61
51DAP/34DAP	1.25016	0.949
52DAP/51DAP	0.94022	1
53DAP/52DAP	0.9882	0.917
55DAP/53DAP	1.31367	0.056
57DAP/55DAP	1.08682	0.841
62DAP/57DAP	1.0674	0.935
68DAP/62DAP	0.87309	0.668
68DAP/14DAP	0.91417	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.84841	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.34815	0.016
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.05496	0.224
Mature Eggplant/Ripe Tomato	0.03113	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.39628	0.591
1-1-2/M82	1.14516	1
12-2/M82	0.58153	0.678
12-4/M82	1.21035	1
1-3/M82	3.25158	0.479
2-1-1/M82	0.83917	1
2-1/M82	N/A	N/A
2-6/M82	2.1386	0.329
3-2/M82	2.0696
4-1-1/M82	2.19242	0.938
4-1/M82	1.01748
4-3-2/M82	2.61093	0.241
4-3/M82	3.18047	0.268
5-3/M82	0.487	0.642
6-2/M82	1.44327	1
6-3/M82	1.52698	1
7-1/M82	1.17313	1
7-2/M82	1.53071	0.385
9-3-2/M82	1.83134

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02025	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.23011	1
IL12-4/WTpooled	1.05314	0.891
IL1-4/WTpooled	1.19147
WT/WTpooled	0.95947	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	1.00169	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.82666	0.839
DC3000/delta hrp 6h	0.66966	0.81
DC3000/delta hrp 12h	1.26522	1
DC3000/delta hrp 24h	0.98635	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08254	0.313
DC3000 delta B/DC3000 delta AB	1.06541	0.51

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	1.04242	1
Var 0h	1.23597	0.98
Var 12h I row2-row1	1.04792	0.795
Var 12h NI row2-row1	1.15438	1
Var 36h I row2-row1	1.18227	0.309
Var 36h NI row2-row1	0.66141	0.706
Var 60h I row2-row1	1.26044	1
Var 60h NI row2-row1	0.90128	0.458
Time course 0hI-0hNI	0.91177	0.204
Time course 12hI-12hNI	1.06656	0.867
Time course 36hI-36hNI	1.13016	0.28
Time course 60hI-60hNI	1.18418	0.033

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)	1.1831	0.339
transgenic ySAMdc/azygous control (breaker)	0.47014	0.15
transgenic ySAMdc/azygous control (red)	1.0455	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91675	0.043

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.951	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.42202	0.172
Manapal/WT (break)	1.66849	0.381
Manapal/WT (red)	1.37724	0.15