Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99683	0.847
27DAP/17DAP	1.3137	0.755
39DAP/27DAP	0.85424	0.529
41DAP/39DAP	1.64276	0.38
42DAP/41DAP	1.08466	1
43DAP/42DAP	1.05496	1
47DAP/43DAP	1.01979	0.902
52DAP/47DAP	1.179	0.757
57DAP/52DAP	0.9463	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94271	0.238
17DAP/reference	1.05434	0.053
27DAP/reference	1.0081	0.934
39DAP/reference	1.03527	0.593
41DAP/reference	0.97101	0.667
42DAP/reference	0.84688	0.012
43DAP/reference	1.0244	0.596
47DAP/reference	0.98942	0.445
52DAP/reference	0.91308	0.177
57DAP/reference	0.77373	0.078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01762	0.899
27DAP/17DAP	0.93918	0.878
39DAP/27DAP	0.97829	0.804
41DAP/39DAP	1.07378	0.883
42DAP/41DAP	0.93373	0.481
43DAP/42DAP	1.06084	0.513
47DAP/43DAP	1.01637	0.948
52DAP/47DAP	1.04916	0.831
57DAP/52DAP	0.9222	0.467
57DAP/7DAP	0.97135	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89321	0.129
17DAP/reference	0.85698	0.108
27DAP/reference	0.96747	0.43
39DAP/reference	0.85941	0.064
41DAP/reference	0.87505	0.056
42DAP/reference	0.76525	0.016
43DAP/reference	0.80934	0.021
47DAP/reference	0.88856	0.168
52DAP/reference	0.84598	0.061
57DAP/reference	0.86131	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04361	0.724
17DAP/reference	0.93814	0.149
27DAP/reference	0.86717	0.134
39DAP/reference	0.86806	0.129
41DAP/reference	0.83962	0.049
42DAP/reference	0.82666	0.073
43DAP/reference	1.16031	0.373
47DAP/reference	0.92371	0.141
52DAP/reference	0.99352	0.619
57DAP/reference	1.06209	0.252

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99189	0.699
17DAP/reference	0.91015	0.308
27DAP/reference	0.82406	0.041
39DAP/reference	0.89879	0.029
41DAP/reference	0.96601	0.56
42DAP/reference	0.89218	0.361
43DAP/reference	0.84642	0.165
47DAP/reference	0.90314	0.174
52DAP/reference	0.82221	0.144
57DAP/reference	0.50151	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99425	1
26DAP/20DAP	0.85387	0.512
34DAP/26DAP	1.05668	1
51DAP/34DAP	0.98607	0.844
52DAP/51DAP	1.14055	0.454
53DAP/52DAP	0.69211	0.063
55DAP/53DAP	1.07739	0.782
57DAP/55DAP	1.19532	0.745
62DAP/57DAP	1.14125	0.622
68DAP/62DAP	1.05166	0.914
68DAP/14DAP	0.93814	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72045	0.042

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.40246	0.814
Immature Eggplant/Mature Eggplant	1.62895	0.507
Ripe Pepper/Ripe Tomato	5.27599
Mature Eggplant/Ripe Tomato	6.41241

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16883
1-1-2/M82	0.79078
12-2/M82	N/A	N/A
12-4/M82	0.97945	1
1-3/M82	0.62938	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.02337
3-2/M82	0.68132
4-1-1/M82	N/A	N/A
4-1/M82	0.67185
4-3-2/M82	0.76896	1
4-3/M82	N/A	N/A
5-3/M82	0.93708
6-2/M82	N/A	N/A
6-3/M82	1.12061	1
7-1/M82	0.74242
7-2/M82	0.84625
9-3-2/M82	0.70064	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87201	0.243
IL2-6/WTpooled	0.93779	0.348
IL7-5/WTpooled	0.95719	1
IL7-3/WTpooled	0.78129	0.418
IL12-4/WTpooled	0.9828	1
IL1-4/WTpooled	0.99088	1
WT/WTpooled	0.96637	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	0.91039	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01107	1
DC3000/delta hrp 6h	0.94401	0.95
DC3000/delta hrp 12h	1.09058	1
DC3000/delta hrp 24h	0.79797	0.092

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51299
DC3000 delta B/DC3000 delta AB	1.00003	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95216	1
Exp 36h	0.85072	0.266
Exp 60h	0.88408	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92612	1
Var 0h	1.13281	0.98
Var 12h I row2-row1	1.09817	0.473
Var 12h NI row2-row1	0.80016	0.494
Var 36h I row2-row1	0.9712	1
Var 36h NI row2-row1	1.1464	1
Var 60h I row2-row1	1.26373	0.562
Var 60h NI row2-row1	1.18788	0.904
Time course 0hI-0hNI	1.01865	1
Time course 12hI-12hNI	0.89216	0.219
Time course 36hI-36hNI	0.69686	0.024
Time course 60hI-60hNI	0.52037	0.005

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)	0.75719	0.454
transgenic ySAMdc/azygous control (breaker)	2.07009	1
transgenic ySAMdc/azygous control (red)	1.67151	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99524	0.757

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)	1.81226	0.105
Manapal/WT (break)	1.48696	0.14
Manapal/WT (red)	1.20828	1