Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89351	0.486
27DAP/17DAP	1.02142	1
39DAP/27DAP	1.02302	1
41DAP/39DAP	0.57496	0.042
42DAP/41DAP	0.92972	1
43DAP/42DAP	1.07249	1
47DAP/43DAP	0.69988	0.2
52DAP/47DAP	2.34785	0.082
57DAP/52DAP	0.89378	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15013	0.17
17DAP/reference	0.82783	0.022
27DAP/reference	1.0801	0.529
39DAP/reference	0.80334	0.034
41DAP/reference	0.75559	0.031
42DAP/reference	1.64491	0.001
43DAP/reference	0.9463	0.377
47DAP/reference	0.95759	0.345
52DAP/reference	1.05184	0.548
57DAP/reference	0.9224	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95693	0.526
27DAP/17DAP	1.1667	0.246
39DAP/27DAP	0.78081	0.069
41DAP/39DAP	0.90475	0.713
42DAP/41DAP	0.94779	0.595
43DAP/42DAP	0.86808	0.068
47DAP/43DAP	0.95174	0.75
52DAP/47DAP	0.88517	0.565
57DAP/52DAP	1.00207	0.857
57DAP/7DAP	1.15665	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98776	0.682
17DAP/reference	1.1363	0.328
27DAP/reference	0.93684	0.283
39DAP/reference	0.88106	0.056
41DAP/reference	0.99301	0.646
42DAP/reference	0.88781	0.189
43DAP/reference	1.47466	0.012
47DAP/reference	0.827	0.168
52DAP/reference	1.14576	0.139
57DAP/reference	2.03737	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80713	0.037
17DAP/reference	1.03398	0.892
27DAP/reference	1.17157	0.562
39DAP/reference	1.05992	0.912
41DAP/reference	1.4528	0.007
42DAP/reference	1.02299	1
43DAP/reference	0.9884	0.62
47DAP/reference	1.07995	0.498
52DAP/reference	0.92394	0.302
57DAP/reference	0.94402	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68363	0.036
17DAP/reference	0.97335	0.636
27DAP/reference	1.04919	0.749
39DAP/reference	1.02743	0.836
41DAP/reference	0.89738	0.107
42DAP/reference	1.06139	0.692
43DAP/reference	1.24942	0.105
47DAP/reference	0.978	0.525
52DAP/reference	1.63091	0.034
57DAP/reference	3.08677	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37544	0.966
26DAP/20DAP	2.63659	0.097
34DAP/26DAP	0.77161	0.219
51DAP/34DAP	1.1065	0.637
52DAP/51DAP	0.95741	1
53DAP/52DAP	1.4252	0.08
55DAP/53DAP	1.24065	0.22
57DAP/55DAP	0.83969	0.437
62DAP/57DAP	0.90146	0.681
68DAP/62DAP	0.83781	0.429
68DAP/14DAP	1.09512	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.17445	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.627	0.187
Mature Green Tomato/Ripe Tomato	1.22782	0.119
Immature Eggplant/Mature Eggplant	1.15733	0.105
Ripe Pepper/Ripe Tomato	0.35934	0.224
Mature Eggplant/Ripe Tomato	0.51341	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.53978
1-1-2/M82	1.13472	1
12-2/M82	3.33779	0.519
12-4/M82	0.76201	0.619
1-3/M82	2.14941	0.248
2-1-1/M82	0.77516
2-1/M82	1.78824
2-6/M82	N/A	N/A
3-2/M82	1.02429	1
4-1-1/M82	N/A	N/A
4-1/M82	1.50628
4-3-2/M82	1.4826
4-3/M82	1.14695	1
5-3/M82	0.47356	0.395
6-2/M82	2.79935	0.253
6-3/M82	0.48542
7-1/M82	1.05999	1
7-2/M82	1.32223	0.385
9-3-2/M82	1.25728	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69881	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.8874	0.559
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.94489	1
IL1-4/WTpooled	1.01407	1
WT/WTpooled	N/A	N/A

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	1.36091	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97512	1
DC3000/delta hrp 6h	1.82484
DC3000/delta hrp 12h	1.2479	1
DC3000/delta hrp 24h	1.02401	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34701	0.063
DC3000 delta B/DC3000 delta AB	1.50995	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12086	1
Exp 36h	1.12249	1
Exp 60h	1.4188	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05048	1
Var 0h	0.97644	1
Var 12h I row2-row1	0.89224	0.514
Var 12h NI row2-row1	1.92953	1
Var 36h I row2-row1	1.34728	0.908
Var 36h NI row2-row1	0.91147	0.743
Var 60h I row2-row1	0.92562	0.292
Var 60h NI row2-row1	0.87205	0.866
Time course 0hI-0hNI	1.17764	0.451
Time course 12hI-12hNI	1.01842	0.876
Time course 36hI-36hNI	1.39288	0.012
Time course 60hI-60hNI	2.3375	0.008

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)	1.56362	0.246
transgenic ySAMdc/azygous control (breaker)	0.45575	0.132
transgenic ySAMdc/azygous control (red)	0.96028	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04805	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.14362	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74647	0.172
Manapal/WT (break)	0.73025	1
Manapal/WT (red)	0.50449	0.274