Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.17.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95306	0.671
27DAP/17DAP	0.75797	0.467
39DAP/27DAP	1.08668	0.899
41DAP/39DAP	0.90917	0.617
42DAP/41DAP	1.14614	0.888
43DAP/42DAP	1.05999	0.937
47DAP/43DAP	1.06474	0.856
52DAP/47DAP	0.99174	0.873
57DAP/52DAP	1.56278	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0022	0.756
17DAP/reference	1.12913	0.051
27DAP/reference	0.94069	0.304
39DAP/reference	1.02137	0.557
41DAP/reference	1.04021	0.91
42DAP/reference	0.83393	0.001
43DAP/reference	1.03509	0.646
47DAP/reference	0.93421	0.083
52DAP/reference	0.9385	0.275
57DAP/reference	0.83786	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80232	0.148
27DAP/17DAP	1.16552	0.61
39DAP/27DAP	0.97313	0.821
41DAP/39DAP	0.95122	0.923
42DAP/41DAP	0.99921	0.795
43DAP/42DAP	0.97523	0.801
47DAP/43DAP	1.04301	0.88
52DAP/47DAP	0.81011	0.316
57DAP/52DAP	1.18937	0.497
57DAP/7DAP	1.7359	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11388	0.435
17DAP/reference	1.22019	0.688
27DAP/reference	0.91482	0.146
39DAP/reference	1.18473	0.12
41DAP/reference	1.02068	1
42DAP/reference	1.15657	0.405
43DAP/reference	1.26814	0.157
47DAP/reference	1.14813	0.604
52DAP/reference	1.13641	0.352
57DAP/reference	0.95339	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10863	0.38
17DAP/reference	0.98232	0.594
27DAP/reference	0.92444	0.24
39DAP/reference	0.87315	0.108
41DAP/reference	0.83987	0.046
42DAP/reference	0.8144	0.039
43DAP/reference	1.03011	0.875
47DAP/reference	0.9091	0.12
52DAP/reference	0.98066	0.433
57DAP/reference	1.24785	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03804	0.616
17DAP/reference	0.96671	0.579
27DAP/reference	1.03374	0.749
39DAP/reference	1.15945	0.091
41DAP/reference	1.15236	0.181
42DAP/reference	0.92503	0.445
43DAP/reference	0.88976	0.256
47DAP/reference	0.91345	0.12
52DAP/reference	1.93983	0.155
57DAP/reference	0.9685	0.394

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05134	0.966
26DAP/20DAP	1.61199	0.117
34DAP/26DAP	1.02663	1
51DAP/34DAP	1.74677	0.207
52DAP/51DAP	1.17795	0.396
53DAP/52DAP	1.00143	1
55DAP/53DAP	1.07793	1
57DAP/55DAP	0.75774	0.238
62DAP/57DAP	1.10487	0.935
68DAP/62DAP	1.19357	0.827
68DAP/14DAP	0.83205	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.52702	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94763	0.726
Mature Green Tomato/Ripe Tomato	0.96152	0.66
Immature Eggplant/Mature Eggplant	1.18679	0.683
Ripe Pepper/Ripe Tomato	0.91642	1
Mature Eggplant/Ripe Tomato	1.38018	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.05348
12-2/M82	N/A	N/A
12-4/M82	0.82193	0.358
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.03529	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.08671	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63323	0.243
IL2-6/WTpooled	1.46384	0.395
IL7-5/WTpooled	1.0278	1
IL7-3/WTpooled	0.47522	0.294
IL12-4/WTpooled	1.02187	0.891
IL1-4/WTpooled	1.01138	1
WT/WTpooled	0.91424	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	0.93222	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9009	0.62
DC3000/delta hrp 6h	1.15348	0.95
DC3000/delta hrp 12h	0.98261	1
DC3000/delta hrp 24h	1.2389	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04375
DC3000 delta B/DC3000 delta AB	0.71002

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09409	1
Exp 36h	1.46498	0.693
Exp 60h	1.18019	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03876	1
Var 0h	1.06138	0.594
Var 12h I row2-row1	1.03808	0.736
Var 12h NI row2-row1	1.27023	0.281
Var 36h I row2-row1	1.07564	0.908
Var 36h NI row2-row1	1.14532	1
Var 60h I row2-row1	0.79871	0.306
Var 60h NI row2-row1	0.89073	0.756
Time course 0hI-0hNI	1.03291	0.852
Time course 12hI-12hNI	1.04015	0.788
Time course 36hI-36hNI	1.55934	0.01
Time course 60hI-60hNI	2.39891	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)	1.00691	0.921
transgenic ySAMdc/azygous control (breaker)	1.05321	1
transgenic ySAMdc/azygous control (red)	1.08943	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97897	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92245	1
Manapal/WT (break)	0.82818	0.333
Manapal/WT (red)	0.99173	0.863