Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96803	0.61
27DAP/17DAP	0.90593	0.8
39DAP/27DAP	1.44188	0.149
41DAP/39DAP	0.88012	0.506
42DAP/41DAP	0.92505	1
43DAP/42DAP	1.0646	1
47DAP/43DAP	0.77947	0.321
52DAP/47DAP	0.87533	0.637
57DAP/52DAP	1.1722	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14167	0.105
17DAP/reference	1.09162	0.166
27DAP/reference	1.31046	0.012
39DAP/reference	1.24756	0.062
41DAP/reference	1.12171	0.067
42DAP/reference	1.06234	0.252
43DAP/reference	0.97197	0.653
47DAP/reference	0.8817	0.027
52DAP/reference	0.8188	0.018
57DAP/reference	0.86506	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92031	0.363
27DAP/17DAP	1.01677	0.96
39DAP/27DAP	0.84835	0.119
41DAP/39DAP	1.37928	0.883
42DAP/41DAP	1.06974	0.947
43DAP/42DAP	0.87221	0.056
47DAP/43DAP	0.98625	0.939
52DAP/47DAP	0.58983	0.041
57DAP/52DAP	0.9753	0.784
57DAP/7DAP	0.3972	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19749	0.091
17DAP/reference	1.25229	0.011
27DAP/reference	1.2794	0.011
39DAP/reference	1.18274	0.042
41DAP/reference	1.06045	0.791
42DAP/reference	1.14512	0.132
43DAP/reference	0.95232	0.305
47DAP/reference	0.81868	0.05
52DAP/reference	0.83208	0.066
57DAP/reference	0.84052	0.048

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1899	0.048
17DAP/reference	1.27119	0.033
27DAP/reference	1.15252	0.23
39DAP/reference	1.05016	0.868
41DAP/reference	0.97387	0.393
42DAP/reference	1.01245	1
43DAP/reference	0.9149	0.135
47DAP/reference	0.85924	0.038
52DAP/reference	0.94405	0.171
57DAP/reference	0.97049	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11014	0.176
17DAP/reference	1.17809	0.279
27DAP/reference	1.22216	0.131
39DAP/reference	1.33259	0.012
41DAP/reference	1.16112	0.044
42DAP/reference	0.86359	0.019
43DAP/reference	0.77604	0.037
47DAP/reference	1.08044	0.155
52DAP/reference	0.91234	0.415
57DAP/reference	1.07077	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92589	1
26DAP/20DAP	2.5277	0.099
34DAP/26DAP	0.85364	0.735
51DAP/34DAP	1.05108	0.927
52DAP/51DAP	1.10467	0.689
53DAP/52DAP	0.75232	0.27
55DAP/53DAP	0.95436	0.796
57DAP/55DAP	0.92878	0.638
62DAP/57DAP	1.29417	0.257
68DAP/62DAP	0.84596	0.314
68DAP/14DAP	0.76975	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.59724	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.15444	0.058
Mature Green Tomato/Ripe Tomato	1.90762	0.015
Immature Eggplant/Mature Eggplant	1.20077	0.248
Ripe Pepper/Ripe Tomato	1.06631	1
Mature Eggplant/Ripe Tomato	5.94321	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28866
1-1-2/M82	1.14721	1
12-2/M82	1.09859
12-4/M82	1.13664	1
1-3/M82	1.0122
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.63398
3-2/M82	0.9799	1
4-1-1/M82	N/A	N/A
4-1/M82	1.03822
4-3-2/M82	1.28653	0.253
4-3/M82	0.7226
5-3/M82	1.29244	1
6-2/M82	1.48023	0.198
6-3/M82	0.72731
7-1/M82	0.78472	0.476
7-2/M82	1.22748
9-3-2/M82	1.16707	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23791	0.254
IL2-6/WTpooled	1.71458	0.395
IL7-5/WTpooled	0.66338	1
IL7-3/WTpooled	0.89248	0.418
IL12-4/WTpooled	1.22866	0.525
IL1-4/WTpooled	1.10566	1
WT/WTpooled	1.06282	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	1.13046	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84179	0.941
DC3000/delta hrp 6h	1.00346	0.95
DC3000/delta hrp 12h	0.99814	1
DC3000/delta hrp 24h	0.70053	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35298	0.042
DC3000 delta B/DC3000 delta AB	1.40392	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89224	0.328
Exp 36h	0.77841	0.406
Exp 60h	0.71555	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9997	1
Var 0h	1.45197	1
Var 12h I row2-row1	0.97083	0.856
Var 12h NI row2-row1	1.07171	0.649
Var 36h I row2-row1	1.18146	0.908
Var 36h NI row2-row1	1.07372	1
Var 60h I row2-row1	0.68985	0.293
Var 60h NI row2-row1	0.85626	0.818
Time course 0hI-0hNI	1.0365	0.852
Time course 12hI-12hNI	1.03405	0.861
Time course 36hI-36hNI	1.32216	0.011
Time course 60hI-60hNI	2.602	0.008

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)	1.00698	1
transgenic ySAMdc/azygous control (breaker)	1.2298	0.248
transgenic ySAMdc/azygous control (red)	1.105	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00371	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.53693	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12368	0.105
Manapal/WT (break)	2.43211	0.13
Manapal/WT (red)	3.73309	0.137