Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.4.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23508	0.523
27DAP/17DAP	1.22113	0.809
39DAP/27DAP	1.6501	0.094
41DAP/39DAP	0.83987	0.407
42DAP/41DAP	1.06943	0.978
43DAP/42DAP	1.12211	1
47DAP/43DAP	1.49323	0.23
52DAP/47DAP	0.58275	0.133
57DAP/52DAP	1.16887	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81043	0.039
17DAP/reference	0.9105	0.085
27DAP/reference	1.03778	0.735
39DAP/reference	1.06623	0.557
41DAP/reference	0.98019	0.667
42DAP/reference	0.93292	0.091
43DAP/reference	1.02416	0.866
47DAP/reference	1.01523	0.91
52DAP/reference	0.99562	0.689
57DAP/reference	1.06481	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16038	0.99
27DAP/17DAP	0.70725
39DAP/27DAP	1.3902
41DAP/39DAP	N/A	N/A
42DAP/41DAP	0.73161	0.238
43DAP/42DAP	1.30723	0.83
47DAP/43DAP	1.24703	0.257
52DAP/47DAP	1.02641	0.951
57DAP/52DAP	0.57876	0.407
57DAP/7DAP	1.17716	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93373	0.326
17DAP/reference	1.03764	1
27DAP/reference	1.08135	0.551
39DAP/reference	0.96728	0.474
41DAP/reference	1.09695	0.475
42DAP/reference	1.05787	0.686
43DAP/reference	1.29925	0.034
47DAP/reference	1.09129	0.67
52DAP/reference	0.82281	0.033
57DAP/reference	0.94696	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98451	0.756
17DAP/reference	0.72674	0.036
27DAP/reference	0.79508	0.155
39DAP/reference	0.88111	0.022
41DAP/reference	1.03122	1
42DAP/reference	1.00389	1
43DAP/reference	1.0859	0.885
47DAP/reference	1.00151	0.749
52DAP/reference	1.22735	0.417
57DAP/reference	0.65648	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13233	0.481
17DAP/reference	0.95962	0.537
27DAP/reference	1.17875	0.07
39DAP/reference	0.93336	0.179
41DAP/reference	0.94786	0.417
42DAP/reference	0.95993	0.552
43DAP/reference	0.83687	0.092
47DAP/reference	1.00297	0.708
52DAP/reference	0.92487	0.482
57DAP/reference	0.99596	0.765

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07171	0.966
26DAP/20DAP	0.12481
34DAP/26DAP	1.40592	1
51DAP/34DAP	1.46809	0.719
52DAP/51DAP	0.47208	0.151
53DAP/52DAP	1.28786	0.565
55DAP/53DAP	0.83253	0.026
57DAP/55DAP	0.75233	0.197
62DAP/57DAP	0.4753	0.05
68DAP/62DAP	1.63834	0.422
68DAP/14DAP	2.10297	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15126

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54832	0.124
Mature Green Tomato/Ripe Tomato	0.64914	0.132
Immature Eggplant/Mature Eggplant	3.14396	0.05
Ripe Pepper/Ripe Tomato	0.80012	0.293
Mature Eggplant/Ripe Tomato	0.51496	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.41764	0.742
1-1-2/M82	1.10414	1
12-2/M82	1.26612	0.336
12-4/M82	1.02184	1
1-3/M82	1.47066	0.255
2-1-1/M82	0.90668	0.784
2-1/M82	1.07087	1
2-6/M82	1.11787	0.594
3-2/M82	1.12165	0.967
4-1-1/M82	0.86503	1
4-1/M82	0.76483
4-3-2/M82	0.97063	1
4-3/M82	1.2142	1
5-3/M82	0.71168	0.49
6-2/M82	1.20093
6-3/M82	1.03142	1
7-1/M82	0.72573	0.452
7-2/M82	0.83113	0.796
9-3-2/M82	1.31279	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.68617
IL2-6/WTpooled	1.04055	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.66498	0.294
IL12-4/WTpooled	1.08264	1
IL1-4/WTpooled	0.94138
WT/WTpooled	1.0235	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96801	1
DC3000/delta hrp 6h	0.78024	0.95
DC3000/delta hrp 12h	0.9712	1
DC3000/delta hrp 24h	0.97235	0.851

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	0.90016	0.328
Exp 36h	1.04302	0.693
Exp 60h	1.21488	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.94508	0.244
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.413	0.264
transgenic ySAMdc/azygous control (breaker)	1.13254	1
transgenic ySAMdc/azygous control (red)	0.88144	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08569	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8367	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08181	0.307
Manapal/WT (break)	0.70804	0.333
Manapal/WT (red)	0.82618	0.36