Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.6.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95985	0.728
27DAP/17DAP	1.07438	0.871
39DAP/27DAP	0.8514	0.458
41DAP/39DAP	1.44661	0.282
42DAP/41DAP	1.08465	1
43DAP/42DAP	1.05786	1
47DAP/43DAP	1.16407	0.438
52DAP/47DAP	1.1817	0.652
57DAP/52DAP	0.9509	0.857

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92669	0.402
17DAP/reference	1.10585	0.048
27DAP/reference	0.96667	0.581
39DAP/reference	1.07793	0.165
41DAP/reference	1.0292	0.759
42DAP/reference	0.92061	0.056
43DAP/reference	0.96811	0.653
47DAP/reference	0.94599	0.137
52DAP/reference	0.86233	0.044
57DAP/reference	0.87089	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96825	0.629
27DAP/17DAP	0.99879	0.969
39DAP/27DAP	1.05062	0.596
41DAP/39DAP	1.05127	0.801
42DAP/41DAP	0.99425	0.887
43DAP/42DAP	1.0097	1
47DAP/43DAP	1.01185	0.957
52DAP/47DAP	1.03978	0.835
57DAP/52DAP	0.92339	0.282
57DAP/7DAP	1.06444	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40989	0.163
17DAP/reference	1.77663	0.011
27DAP/reference	2.28127	0.006
39DAP/reference	2.69428	0.006
41DAP/reference	3.10374	0.011
42DAP/reference	2.18643	0.014
43DAP/reference	2.22764	0.007
47DAP/reference	1.40936	0.285
52DAP/reference	2.20827	0.007
57DAP/reference	1.78653	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11552	0.304
17DAP/reference	1.06807	0.448
27DAP/reference	1.12853	0.265
39DAP/reference	0.9404	0.322
41DAP/reference	0.93943	0.262
42DAP/reference	0.93348	0.15
43DAP/reference	1.05569	0.892
47DAP/reference	0.8876	0.049
52DAP/reference	1.04797	0.789
57DAP/reference	1.1018	0.567

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59792	0.031
17DAP/reference	1.34829	0.137
27DAP/reference	1.63217	0.051
39DAP/reference	1.65617	0.019
41DAP/reference	1.70113	0.029
42DAP/reference	1.50336	0.035
43DAP/reference	1.50195	0.264
47DAP/reference	0.97776	0.538
52DAP/reference	2.0233	0.105
57DAP/reference	1.10143	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92484	1
26DAP/20DAP	0.90907	0.512
34DAP/26DAP	1.05081	1
51DAP/34DAP	1.0208	0.883
52DAP/51DAP	1.03909	0.704
53DAP/52DAP	0.84887	0.167
55DAP/53DAP	0.96735	0.761
57DAP/55DAP	1.10948	0.779
62DAP/57DAP	1.22773	0.002
68DAP/62DAP	1.07362	1
68DAP/14DAP	0.7755	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99143	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.79095	0.058
Mature Green Tomato/Ripe Tomato	0.9366	0.487
Immature Eggplant/Mature Eggplant	1.25013	0.11
Ripe Pepper/Ripe Tomato	6.24853
Mature Eggplant/Ripe Tomato	2.19053

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04556	1
1-1-2/M82	0.98099	1
12-2/M82	0.89703	0.955
12-4/M82	0.95255	1
1-3/M82	0.97653	0.501
2-1-1/M82	1.20354	0.764
2-1/M82	1.19709	1
2-6/M82	1.03849	0.594
3-2/M82	0.96644
4-1-1/M82	0.92198	1
4-1/M82	1.00012	1
4-3-2/M82	0.84773	0.487
4-3/M82	1.02258	1
5-3/M82	0.99367	1
6-2/M82	1.31826
6-3/M82	1.00048	1
7-1/M82	1.10689	1
7-2/M82	0.99302	1
9-3-2/M82	0.87021	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.28849	0.277
IL2-6/WTpooled	1.45943
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86739	1
IL12-4/WTpooled	0.75837	0.566
IL1-4/WTpooled	1.21111	1
WT/WTpooled	0.9245	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	1.01109	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91221	1
DC3000/delta hrp 6h	0.8573	0.95
DC3000/delta hrp 12h	0.94887	1
DC3000/delta hrp 24h	1.03674	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1331	0.063
DC3000 delta B/DC3000 delta AB	1.08328	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97996	1
Exp 36h	1.4709	1
Exp 60h	0.9325	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01368	1
Var 0h	1.25314	0.594
Var 12h I row2-row1	1.15654	0.254
Var 12h NI row2-row1	1.07244	1
Var 36h I row2-row1	0.92876	1
Var 36h NI row2-row1	0.9758	0.791
Var 60h I row2-row1	1.23409	1
Var 60h NI row2-row1	1.1591	0.904
Time course 0hI-0hNI	1.0506	0.867
Time course 12hI-12hNI	1.025	0.82
Time course 36hI-36hNI	0.92792	0.215
Time course 60hI-60hNI	1.12961	0.06

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)	1.13149	0.272
transgenic ySAMdc/azygous control (breaker)	0.89999	0.251
transgenic ySAMdc/azygous control (red)	0.97143	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05337	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76964	1
Manapal/WT (break)	1.12581	1
Manapal/WT (red)	1.21214	1