Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.15.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67224	0.131
27DAP/17DAP	1.14556	0.849
39DAP/27DAP	1.47839	0.201
41DAP/39DAP	1.03863	0.982
42DAP/41DAP	1.75935	0.169
43DAP/42DAP	1.18579	1
47DAP/43DAP	0.95552	0.744
52DAP/47DAP	0.94137	0.758
57DAP/52DAP	1.05861	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91537	0.132
17DAP/reference	1.0349	0.258
27DAP/reference	0.99843	0.885
39DAP/reference	1.0488	0.157
41DAP/reference	1.02684	0.91
42DAP/reference	0.95147	0.095
43DAP/reference	1.05131	0.252
47DAP/reference	1.0299	0.685
52DAP/reference	0.99801	0.654
57DAP/reference	0.94442	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28208	0.121
27DAP/17DAP	1.1072	0.653
39DAP/27DAP	2.99437	0.045
41DAP/39DAP	1.77241	0.232
42DAP/41DAP	1.40169	0.635
43DAP/42DAP	0.9909	0.801
47DAP/43DAP	4.00932	0.015
52DAP/47DAP	0.92155	0.666
57DAP/52DAP	2.40294	0.029
57DAP/7DAP	33.7022	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.81046	0.076
17DAP/reference	1.52751	0.035
27DAP/reference	1.12135	0.664
39DAP/reference	1.81835	0.007
41DAP/reference	1.51231	0.011
42DAP/reference	1.9027	0.009
43DAP/reference	1.38067	0.212
47DAP/reference	1.23309	0.229
52DAP/reference	1.52742	0.017
57DAP/reference	1.37533	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00141	0.993
17DAP/reference	0.88919	0.004
27DAP/reference	0.89193	0.09
39DAP/reference	0.90561	0.097
41DAP/reference	0.98136	0.441
42DAP/reference	0.93208	0.189
43DAP/reference	1.34894	0.343
47DAP/reference	1.04661	0.256
52DAP/reference	0.94541	0.156
57DAP/reference	0.93826	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12842	0.207
17DAP/reference	1.16528	0.362
27DAP/reference	1.59631	0.02
39DAP/reference	1.37048	0.038
41DAP/reference	1.2243	0.047
42DAP/reference	1.00057	0.816
43DAP/reference	1.16962	0.505
47DAP/reference	0.94422	0.259
52DAP/reference	1.16739	0.592
57DAP/reference	1.02339	0.858

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97332	1
26DAP/20DAP	1.05331	1
34DAP/26DAP	0.57969	0.083
51DAP/34DAP	1.11184	0.814
52DAP/51DAP	1.34203	0.033
53DAP/52DAP	4.54471	0.019
55DAP/53DAP	3.07986	0.027
57DAP/55DAP	2.21448	0.301
62DAP/57DAP	0.59138	0.05
68DAP/62DAP	1.52233	0.682
68DAP/14DAP	0.92306	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.44007	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.90725	0.458
Mature Green Tomato/Ripe Tomato	0.85988	0.347
Immature Eggplant/Mature Eggplant	2.73852	0.05
Ripe Pepper/Ripe Tomato	1.11272	1
Mature Eggplant/Ripe Tomato	2.22116	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11308	0.877
1-1-2/M82	0.92956	1
12-2/M82	1.22749	0.61
12-4/M82	0.76703	1
1-3/M82	1.95945
2-1-1/M82	0.86674
2-1/M82	2.26919	0.345
2-6/M82	0.79778	1
3-2/M82	N/A	N/A
4-1-1/M82	1.15439	1
4-1/M82	1.36921	1
4-3-2/M82	2.88448
4-3/M82	N/A	N/A
5-3/M82	2.34085	0.572
6-2/M82	5.35682
6-3/M82	0.78514	1
7-1/M82	1.39611
7-2/M82	1.79154	0.318
9-3-2/M82	1.52569	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.34048	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.89457	1
IL12-4/WTpooled	1.47596	0.538
IL1-4/WTpooled	0.94643	1
WT/WTpooled	0.96584	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	1.93554	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91255	0.664
DC3000/delta hrp 6h	1.01606	0.95
DC3000/delta hrp 12h	1.04451	1
DC3000/delta hrp 24h	0.91105	0.513

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2895	0.121
DC3000 delta B/DC3000 delta AB	1.69616	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0925	0.254
Exp 36h	2.04928	0.693
Exp 60h	1.42705	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04543	1
Var 0h	1.05591	0.263
Var 12h I row2-row1	1.7065	0.613
Var 12h NI row2-row1	1.68322	0.34
Var 36h I row2-row1	0.63055	0.575
Var 36h NI row2-row1	0.79495	0.522
Var 60h I row2-row1	0.82143	0.832
Var 60h NI row2-row1	0.99618	1
Time course 0hI-0hNI	1.1299	0.719
Time course 12hI-12hNI	1.1979	0.482
Time course 36hI-36hNI	3.62718	0.004
Time course 60hI-60hNI	14.5375	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)	0.98921	0.722
transgenic ySAMdc/azygous control (breaker)	1.14198	0.178
transgenic ySAMdc/azygous control (red)	1.04733	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98419	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98124	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77406	1
Manapal/WT (break)	0.89062	0.299
Manapal/WT (red)	0.46095	0.36