Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42044	0.365
27DAP/17DAP	0.80638	0.583
39DAP/27DAP	0.73066	0.507
41DAP/39DAP	1.10505	0.642
42DAP/41DAP	1.68648	0.169
43DAP/42DAP	0.91952	0.851
47DAP/43DAP	1.15781	0.459
52DAP/47DAP	1.02763	0.916
57DAP/52DAP	1.23934	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8733	0.205
17DAP/reference	1.16037	0.27
27DAP/reference	0.98596	0.711
39DAP/reference	1.14724	0.386
41DAP/reference	1.09977	0.759
42DAP/reference	1.03653	0.565
43DAP/reference	1.13522	0.325
47DAP/reference	1.16773	0.055
52DAP/reference	0.99684	0.668
57DAP/reference	1.19326	0.153

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23037	0.086
27DAP/17DAP	0.76704	0.418
39DAP/27DAP	0.76746	0.066
41DAP/39DAP	1.01855	1
42DAP/41DAP	0.95579	0.684
43DAP/42DAP	1.20928	0.052
47DAP/43DAP	1.02	1
52DAP/47DAP	0.94918	0.857
57DAP/52DAP	0.82689	0.132
57DAP/7DAP	1.1595	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8673	0.122
17DAP/reference	0.83036	0.028
27DAP/reference	0.88568	0.035
39DAP/reference	1.1522	0.101
41DAP/reference	0.72424	0.032
42DAP/reference	0.7202	0.03
43DAP/reference	0.84807	0.056
47DAP/reference	1.03716	1
52DAP/reference	0.96589	0.213
57DAP/reference	0.82401	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86549	0.374
17DAP/reference	0.93605	0.399
27DAP/reference	1.02658	0.735
39DAP/reference	0.99916	0.702
41DAP/reference	1.1429	0.129
42DAP/reference	1.23111	0.051
43DAP/reference	1.22427	0.086
47DAP/reference	1.26874	0.008
52DAP/reference	1.02781	1
57DAP/reference	1.02666	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03064	0.918
17DAP/reference	1.11689	0.362
27DAP/reference	0.93292	0.357
39DAP/reference	1.02278	0.858
41DAP/reference	0.91291	0.293
42DAP/reference	1.02089	1
43DAP/reference	0.8968	0.256
47DAP/reference	0.97453	0.525
52DAP/reference	0.85518	0.228
57DAP/reference	1.03489	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.003	1
26DAP/20DAP	0.99512	1
34DAP/26DAP	1.09025	1
51DAP/34DAP	0.88311	0.537
52DAP/51DAP	0.7112	0.151
53DAP/52DAP	1.83696	0.356
55DAP/53DAP	1.03652	0.964
57DAP/55DAP	0.90294	0.59
62DAP/57DAP	1.89788	0.393
68DAP/62DAP	1.39491	0.729
68DAP/14DAP	1.68535	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.56133	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.38414	0.081
Mature Green Tomato/Ripe Tomato	5.45395	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	6.95557	1
Mature Eggplant/Ripe Tomato	1.14454	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30083	0.877
1-1-2/M82	0.72969
12-2/M82	0.51067
12-4/M82	0.70656	0.257
1-3/M82	N/A	N/A
2-1-1/M82	1.24523	0.764
2-1/M82	0.73056
2-6/M82	1.45687	0.505
3-2/M82	0.98074	1
4-1-1/M82	1.20184	1
4-1/M82	1.01597
4-3-2/M82	1.81136	0.508
4-3/M82	0.81295	0.72
5-3/M82	0.82757	0.49
6-2/M82	0.63905
6-3/M82	0.87428
7-1/M82	0.82488
7-2/M82	0.98752
9-3-2/M82	1.60584	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.28486
IL2-6/WTpooled	1.09483	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03636	1
IL12-4/WTpooled	1.09141	0.785
IL1-4/WTpooled	1.15417	1
WT/WTpooled	1.08747	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	0.87554	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10302	0.823
DC3000/delta hrp 6h	1.25967	1
DC3000/delta hrp 12h	1.01102	1
DC3000/delta hrp 24h	0.88072	0.1

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	0.47224

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86675	1
Exp 36h	N/A	N/A
Exp 60h	0.85171	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02493	1
Var 0h	1.01382	1
Var 12h I row2-row1	0.86981	0.565
Var 12h NI row2-row1	0.93981	0.546
Var 36h I row2-row1	0.74893	0.805
Var 36h NI row2-row1	1.26239	0.253
Var 60h I row2-row1	0.88438	0.952
Var 60h NI row2-row1	0.95407	1
Time course 0hI-0hNI	1.01424	0.867
Time course 12hI-12hNI	0.99358	1
Time course 36hI-36hNI	0.80569	0.023
Time course 60hI-60hNI	0.40995	0.007

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)	0.83426	0.291
transgenic ySAMdc/azygous control (breaker)	1.63773	0.248
transgenic ySAMdc/azygous control (red)	1.02489	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97694	0.196

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09648	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.58375	0.14
Manapal/WT (break)	1.78585	0.13
Manapal/WT (red)	1.79513	0.222