Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.16.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20708	0.878
27DAP/17DAP	1.15295	0.845
39DAP/27DAP	1.01546	1
41DAP/39DAP	0.82438	0.365
42DAP/41DAP	1.25498	0.871
43DAP/42DAP	0.87217	0.709
47DAP/43DAP	1.30784	0.647
52DAP/47DAP	0.94549	0.765
57DAP/52DAP	1.11585	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88431	0.159
17DAP/reference	0.89131	0.26
27DAP/reference	1.25453	0.033
39DAP/reference	1.14996	0.504
41DAP/reference	0.92757	0.542
42DAP/reference	0.86087	0.002
43DAP/reference	0.96865	0.594
47DAP/reference	0.99059	0.535
52DAP/reference	1.4238	0.019
57DAP/reference	1.42054	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82833	0.27
27DAP/17DAP	1.01752	0.969
39DAP/27DAP	1.39181	0.171
41DAP/39DAP	1.12516	0.896
42DAP/41DAP	1.17403	0.727
43DAP/42DAP	0.97222	0.729
47DAP/43DAP	1.17681	0.798
52DAP/47DAP	1.03381	0.987
57DAP/52DAP	0.93353	0.685
57DAP/7DAP	1.31832	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75594	0.104
17DAP/reference	0.82594	0.064
27DAP/reference	1.05991	0.804
39DAP/reference	0.77027	0.02
41DAP/reference	0.81272	0.025
42DAP/reference	1.22303	0.024
43DAP/reference	1.01342	0.694
47DAP/reference	0.92134	0.101
52DAP/reference	1.03026	0.832
57DAP/reference	0.86118	0.047

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92386	0.457
17DAP/reference	0.77129	0.011
27DAP/reference	0.90943	0.212
39DAP/reference	0.94036	0.195
41DAP/reference	0.94443	0.169
42DAP/reference	0.95583	0.355
43DAP/reference	1.21112	0.598
47DAP/reference	0.85528	0.031
52DAP/reference	1.01143	1
57DAP/reference	0.84851	0.05

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75567	0.036
17DAP/reference	0.96434	0.519
27DAP/reference	0.90068	0.195
39DAP/reference	1.01191	0.935
41DAP/reference	0.95721	0.417
42DAP/reference	1.00978	1
43DAP/reference	0.79592	0.081
47DAP/reference	0.95623	0.315
52DAP/reference	0.83312	0.16
57DAP/reference	1.20125	0.151

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17353	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.03257	1
51DAP/34DAP	1.04411	0.869
52DAP/51DAP	1.00928	1
53DAP/52DAP	1.04601	1
55DAP/53DAP	1.10594	0.741
57DAP/55DAP	1.00464	0.93
62DAP/57DAP	0.91629	0.871
68DAP/62DAP	1.54681	0.198
68DAP/14DAP	1.37454	0.295

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61593	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06577	0.774
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.50208	0.293
Mature Eggplant/Ripe Tomato	0.49904	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.82822	0.402
1-1-2/M82	1.14193	1
12-2/M82	1.01265
12-4/M82	0.77537	0.358
1-3/M82	1.0125
2-1-1/M82	0.80046	0.683
2-1/M82	0.80812
2-6/M82	0.72869	1
3-2/M82	0.83091
4-1-1/M82	0.95	1
4-1/M82	N/A	N/A
4-3-2/M82	0.80899
4-3/M82	1.67467	0.268
5-3/M82	1.08559	1
6-2/M82	0.69288
6-3/M82	1.24035
7-1/M82	N/A	N/A
7-2/M82	0.78674	0.553
9-3-2/M82	0.74326	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.51667	0.243
IL2-6/WTpooled	0.82105	0.473
IL7-5/WTpooled	0.94871	1
IL7-3/WTpooled	1.46549	0.362
IL12-4/WTpooled	1.22614	0.785
IL1-4/WTpooled	0.79483	0.699
WT/WTpooled	1.01047	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	1.05029

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.29878	0.692
DC3000/delta hrp 6h	0.60022
DC3000/delta hrp 12h	1.0229	1
DC3000/delta hrp 24h	1.02595	0.779

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	1.09692	1
Exp 36h	3.04399	1
Exp 60h	1.33335	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01201	1
Var 0h	1.11514	0.936
Var 12h I row2-row1	1.22205	0.187
Var 12h NI row2-row1	0.87347	0.713
Var 36h I row2-row1	0.62221	0.575
Var 36h NI row2-row1	0.92467	0.482
Var 60h I row2-row1	0.97307
Var 60h NI row2-row1	0.65171	1
Time course 0hI-0hNI	0.97834	0.927
Time course 12hI-12hNI	1.02764	0.754
Time course 36hI-36hNI	1.01414	0.89
Time course 60hI-60hNI	0.99092	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)	1.21159	0.748
transgenic ySAMdc/azygous control (breaker)	1.09538	1
transgenic ySAMdc/azygous control (red)	0.86856	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9782	0.156

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95038	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92386	1
Manapal/WT (break)	1.18882	0.14
Manapal/WT (red)	0.8513	0.242