Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13515	0.602
27DAP/17DAP	1.06391	0.88
39DAP/27DAP	1.12153	0.888
41DAP/39DAP	0.79231	0.235
42DAP/41DAP	1.13682	0.825
43DAP/42DAP	1.08452	1
47DAP/43DAP	1.23125	0.527
52DAP/47DAP	0.71441	0.174
57DAP/52DAP	1.07436	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06379	0.994
17DAP/reference	0.85613	0.041
27DAP/reference	0.79089	0.141
39DAP/reference	0.88703	0.381
41DAP/reference	0.7973	0.009
42DAP/reference	1.31123	0.022
43DAP/reference	0.86784	0.073
47DAP/reference	1.88922	0.04
52DAP/reference	1.16388	0.302
57DAP/reference	0.3847

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8176	0.058
27DAP/17DAP	1.11354	0.579
39DAP/27DAP	0.90539	0.334
41DAP/39DAP	0.94301	0.861
42DAP/41DAP	0.95728	0.715
43DAP/42DAP	1.02513	0.554
47DAP/43DAP	0.97075	0.815
52DAP/47DAP	0.92633	0.666
57DAP/52DAP	0.92164	0.596
57DAP/7DAP	0.79206	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87238	0.157
17DAP/reference	0.79004	0.064
27DAP/reference	0.81157	0.026
39DAP/reference	0.87348	0.109
41DAP/reference	0.7826	0.042
42DAP/reference	0.83166	0.082
43DAP/reference	0.8401	0.022
47DAP/reference	1.15706	0.173
52DAP/reference	0.80185	0.077
57DAP/reference	0.83911	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30862	0.463
17DAP/reference	1.27254	0.023
27DAP/reference	1.63516	0.043
39DAP/reference	1.38236	0.077
41DAP/reference	1.52042	0.014
42DAP/reference	1.3095	0.009
43DAP/reference	1.76074	0.424
47DAP/reference	1.11302	0.164
52DAP/reference	1.01542	0.938
57DAP/reference	0.93038	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84243	0.147
17DAP/reference	1.09599	1
27DAP/reference	0.65304	0.05
39DAP/reference	0.91828	0.271
41DAP/reference	0.93457	0.371
42DAP/reference	1.32749	0.233
43DAP/reference	1.45374	0.013
47DAP/reference	1.4075	0.017
52DAP/reference	1.87062	0.04
57DAP/reference	2.06339	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01557	1
26DAP/20DAP	1.11582	1
34DAP/26DAP	0.99549	1
51DAP/34DAP	0.86947	0.311
52DAP/51DAP	1.0255	0.708
53DAP/52DAP	0.99553	0.99
55DAP/53DAP	1.02249	1
57DAP/55DAP	0.97823	0.867
62DAP/57DAP	1.07587	1
68DAP/62DAP	1.29157	0.95
68DAP/14DAP	1.13972	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00318	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32465	0.075
Mature Green Tomato/Ripe Tomato	1.62795	0.095
Immature Eggplant/Mature Eggplant	0.31453	0.063
Ripe Pepper/Ripe Tomato	1.7037	1
Mature Eggplant/Ripe Tomato	2.02103	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88152	0.944
1-1-2/M82	1.32873	1
12-2/M82	N/A	N/A
12-4/M82	0.95643	1
1-3/M82	1.51129	0.277
2-1-1/M82	1.21563	0.457
2-1/M82	1.09365
2-6/M82	1.35638
3-2/M82	1.02108
4-1-1/M82	1.09946	1
4-1/M82	N/A	N/A
4-3-2/M82	1.30853	0.508
4-3/M82	1.17235
5-3/M82	1.2192	0.467
6-2/M82	1.44931
6-3/M82	1.26698
7-1/M82	N/A	N/A
7-2/M82	0.93008
9-3-2/M82	1.3277

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	2.07678
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.95091
WT/WTpooled	N/A	N/A

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	1.0849	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08047	0.921
DC3000/delta hrp 6h	1.13491	1
DC3000/delta hrp 12h	1.29832	1
DC3000/delta hrp 24h	0.75999	0.076

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60922	0.024
DC3000 delta B/DC3000 delta AB	0.6647	0.023

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93435	1
Exp 36h	0.76961	0.449
Exp 60h	0.61171	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00741	1
Var 0h	1.16349	0.374
Var 12h I row2-row1	0.83879	0.39
Var 12h NI row2-row1	1.04968	0.649
Var 36h I row2-row1	1.07846	0.489
Var 36h NI row2-row1	0.84975	0.421
Var 60h I row2-row1	0.87261	0.832
Var 60h NI row2-row1	0.94789	0.866
Time course 0hI-0hNI	1.01199	0.852
Time course 12hI-12hNI	0.93823	0.32
Time course 36hI-36hNI	0.96325	0.36
Time course 60hI-60hNI	0.66213	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)	1.04587	0.511
transgenic ySAMdc/azygous control (breaker)	0.8825	0.15
transgenic ySAMdc/azygous control (red)	0.88472	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03781	0.301

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.6694	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39608	0.084
Manapal/WT (break)	1.65211	0.126
Manapal/WT (red)	1.47798	0.15