Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47621	0.443
27DAP/17DAP	15.5938	0.184
39DAP/27DAP	1.94784	0.078
41DAP/39DAP	1.02725	0.777
42DAP/41DAP	1.07871	0.941
43DAP/42DAP	1.07288	0.937
47DAP/43DAP	1.08901	0.999
52DAP/47DAP	1.27753	0.639
57DAP/52DAP	1.4481	0.348

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02954	0.96
17DAP/reference	1.16026	0.055
27DAP/reference	0.9979	0.822
39DAP/reference	1.142	0.021
41DAP/reference	1.11386	0.145
42DAP/reference	0.93581	0.095
43DAP/reference	0.94728	0.519
47DAP/reference	0.93346	0.077
52DAP/reference	0.83618	0.036
57DAP/reference	0.77625	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84038	0.148
27DAP/17DAP	0.93468	0.748
39DAP/27DAP	1.26626	0.174
41DAP/39DAP	1.00626	1
42DAP/41DAP	0.77198	0.033
43DAP/42DAP	1.00597	1
47DAP/43DAP	1.16632	0.325
52DAP/47DAP	0.8506	0.338
57DAP/52DAP	1.37524	0.333
57DAP/7DAP	1.14705	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11516	0.461
17DAP/reference	0.91972	0.253
27DAP/reference	1.09219	0.551
39DAP/reference	1.06232	0.436
41DAP/reference	0.88988	0.247
42DAP/reference	0.90669	0.248
43DAP/reference	0.97533	0.459
47DAP/reference	1.19669	0.671
52DAP/reference	1.03062	0.563
57DAP/reference	1.32571	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99066	0.831
17DAP/reference	1.01457	0.904
27DAP/reference	0.86246	0.111
39DAP/reference	0.8875	0.289
41DAP/reference	0.94313	0.307
42DAP/reference	0.8523	0.061
43DAP/reference	1.01387	0.831
47DAP/reference	1.05272	0.092
52DAP/reference	0.97576	0.469
57DAP/reference	1.18471	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00401	1
17DAP/reference	1.04263	0.792
27DAP/reference	1.03076	0.871
39DAP/reference	1.06659	0.211
41DAP/reference	1.11096	0.286
42DAP/reference	1.04746	1
43DAP/reference	1.07536	1
47DAP/reference	0.97338	0.509
52DAP/reference	1.36359	0.443
57DAP/reference	0.67637	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18127	0.966
26DAP/20DAP	0.76041	0.205
34DAP/26DAP	0.86016	0.653
51DAP/34DAP	1.29238	0.654
52DAP/51DAP	0.89717
53DAP/52DAP	0.82601	0.649
55DAP/53DAP	1.2489	0.215
57DAP/55DAP	1.05839	0.997
62DAP/57DAP	0.90596	0.162
68DAP/62DAP	0.90945	0.668
68DAP/14DAP	1.02596	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12661	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.32039
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.00053	1
Mature Eggplant/Ripe Tomato	0.11682	0.231

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.17294	0.409
1-1-2/M82	0.87419	1
12-2/M82	1.29307	1
12-4/M82	0.30965	0.319
1-3/M82	N/A	N/A
2-1-1/M82	4.0238	0.375
2-1/M82	6.73747	0.312
2-6/M82	0.62305	1
3-2/M82	N/A	N/A
4-1-1/M82	0.78412	1
4-1/M82	0.4387
4-3-2/M82	0.44486	0.445
4-3/M82	0.75191	0.611
5-3/M82	1.1693	0.572
6-2/M82	0.37101	0.481
6-3/M82	0.68883
7-1/M82	0.63378	0.509
7-2/M82	0.85566
9-3-2/M82	0.80068	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80774	0.247
IL2-6/WTpooled	1.07987	0.659
IL7-5/WTpooled	0.90817	1
IL7-3/WTpooled	0.9107	0.298
IL12-4/WTpooled	1.07498	0.737
IL1-4/WTpooled	1.45095	1
WT/WTpooled	0.96002	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	1.08964	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0041
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.74216	0.028

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	1.57839	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22795	1
Exp 36h	4.3446	0.409
Exp 60h	2.06076	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99648	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.88751	0.467
Var 12h NI row2-row1	0.72303	0.546
Var 36h I row2-row1	1.12716	1
Var 36h NI row2-row1	1.19201	0.253
Var 60h I row2-row1	1.00463	0.562
Var 60h NI row2-row1	1.24577	0.904
Time course 0hI-0hNI	1.02947	0.867
Time course 12hI-12hNI	1.31111	0.682
Time course 36hI-36hNI	1.199	0.316
Time course 60hI-60hNI	1.72976	0.009

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)	1.01442	1
transgenic ySAMdc/azygous control (breaker)	0.91663	1
transgenic ySAMdc/azygous control (red)	1.23781	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04298	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39212	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1901	0.105
Manapal/WT (break)	2.34154	0.183
Manapal/WT (red)	1.48606	0.413