Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6496	0.033
27DAP/17DAP	0.98121	0.952
39DAP/27DAP	2.49767	0.026
41DAP/39DAP	1.04526	0.973
42DAP/41DAP	0.90184	1
43DAP/42DAP	1.27764	1
47DAP/43DAP	1.04757	0.926
52DAP/47DAP	1.17803	0.718
57DAP/52DAP	0.7808	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95056	0.352
17DAP/reference	0.73618	0.01
27DAP/reference	0.80908	0.085
39DAP/reference	0.75794	0.023
41DAP/reference	0.56177	0.01
42DAP/reference	0.91699	0.12
43DAP/reference	1.07393	0.163
47DAP/reference	1.34813	0.001
52DAP/reference	1.21295	0.256
57DAP/reference	1.15719	0.094

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72213	0.099
27DAP/17DAP	1.42023	0.032
39DAP/27DAP	0.85798	0.334
41DAP/39DAP	0.90018	0.729
42DAP/41DAP	1.41577	0.009
43DAP/42DAP	1.13407	0.212
47DAP/43DAP	1.076	0.414
52DAP/47DAP	0.80889	0.065
57DAP/52DAP	0.95215	0.601
57DAP/7DAP	1.16499	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18786	0.129
17DAP/reference	0.89966	0.167
27DAP/reference	0.89375	0.125
39DAP/reference	0.97692	0.552
41DAP/reference	0.98441	0.565
42DAP/reference	1.16302	0.174
43DAP/reference	1.14428	0.241
47DAP/reference	1.18959	0.292
52DAP/reference	1.13411	0.139
57DAP/reference	1.07993	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13265	0.538
17DAP/reference	0.75295	0.01
27DAP/reference	1.17047	0.388
39DAP/reference	1.1346	0.824
41DAP/reference	1.11112	0.72
42DAP/reference	1.02531	1
43DAP/reference	0.80125	0.125
47DAP/reference	0.78704	0.058
52DAP/reference	0.87178	0.187
57DAP/reference	0.91952	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06189	0.918
17DAP/reference	0.99043	0.778
27DAP/reference	0.96457	0.416
39DAP/reference	1.09779	0.691
41DAP/reference	1.24253	0.067
42DAP/reference	1.19202	0.209
43DAP/reference	1.96671	0.013
47DAP/reference	1.33455	0.008
52DAP/reference	1.37427	0.073
57DAP/reference	1.88149	0.01

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29664	0.966
26DAP/20DAP	2.04344	0.097
34DAP/26DAP	0.83057	0.479
51DAP/34DAP	1.20801	0.164
52DAP/51DAP	1.00598	1
53DAP/52DAP	0.77445	0.301
55DAP/53DAP	0.54338	0.016
57DAP/55DAP	1.30457	0.728
62DAP/57DAP	1.7551	0.833
68DAP/62DAP	1.03327	0.939
68DAP/14DAP	2.37445	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60148	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.99804	0.058
Mature Green Tomato/Ripe Tomato	0.36237	0.021
Immature Eggplant/Mature Eggplant	2.49783	0.05
Ripe Pepper/Ripe Tomato	0.55331	0.224
Mature Eggplant/Ripe Tomato	0.40537	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18172	0.742
1-1-2/M82	1.24435	1
12-2/M82	0.94751	0.955
12-4/M82	1.17837	1
1-3/M82	2.12222	0.232
2-1-1/M82	0.9727	1
2-1/M82	0.57449	0.322
2-6/M82	1.50964	0.395
3-2/M82	1.21014	0.426
4-1-1/M82	1.25806	1
4-1/M82	1.92193	1
4-3-2/M82	2.61191	0.246
4-3/M82	2.56457	0.268
5-3/M82	0.9428	1
6-2/M82	1.43307	0.253
6-3/M82	0.98946	1
7-1/M82	0.91596	0.803
7-2/M82	1.50552	0.302
9-3-2/M82	1.86652

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.32155
IL2-6/WTpooled	0.98486	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.85416	0.418
IL12-4/WTpooled	0.82559	0.566
IL1-4/WTpooled	1.26902
WT/WTpooled	0.88879	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	0.97127	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94218	1
DC3000/delta hrp 6h	1.14535	1
DC3000/delta hrp 12h	0.88785	1
DC3000/delta hrp 24h	1.9768	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94009	0.724
DC3000 delta B/DC3000 delta AB	0.80824	0.121

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.28244	0.254
Exp 36h	0.95185	0.82
Exp 60h	0.98551	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98817	1
Var 0h	0.57341	0.332
Var 12h I row2-row1	0.86372	0.338
Var 12h NI row2-row1	1.0673	1
Var 36h I row2-row1	1.05585	1
Var 36h NI row2-row1	1.16126	0.276
Var 60h I row2-row1	0.74967	0.287
Var 60h NI row2-row1	0.9942	1
Time course 0hI-0hNI	0.9945	1
Time course 12hI-12hNI	1.00176	1
Time course 36hI-36hNI	0.99447	0.68
Time course 60hI-60hNI	0.32404	0.006

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)	1.19654	0.267
transgenic ySAMdc/azygous control (breaker)	0.60748	0.139
transgenic ySAMdc/azygous control (red)	1.15018	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91216	0.149

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88908	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.36741	0.083
Manapal/WT (break)	1.84259	0.14
Manapal/WT (red)	2.66536	0.126