Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.15.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70407	0.083
27DAP/17DAP	1.00074	1
39DAP/27DAP	1.47514	0.107
41DAP/39DAP	0.92256	0.641
42DAP/41DAP	1.03147	1
43DAP/42DAP	1.09915	1
47DAP/43DAP	1.10269	0.825
52DAP/47DAP	1.63768	0.306
57DAP/52DAP	1.1639	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.008	1
17DAP/reference	0.99052	0.777
27DAP/reference	1.01438	0.75
39DAP/reference	0.96171	0.35
41DAP/reference	0.96252	0.434
42DAP/reference	0.92804	0.037
43DAP/reference	1.04123	0.152
47DAP/reference	1.00218	0.674
52DAP/reference	1.07776	0.766
57DAP/reference	0.93565	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93437	0.299
27DAP/17DAP	1.02682	0.928
39DAP/27DAP	0.94451	0.311
41DAP/39DAP	0.94523	0.645
42DAP/41DAP	0.94661	0.484
43DAP/42DAP	1.01712	0.351
47DAP/43DAP	0.99564	0.99
52DAP/47DAP	1.00157	1
57DAP/52DAP	0.96265	0.484
57DAP/7DAP	0.88745	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16887	0.11
17DAP/reference	1.02863	1
27DAP/reference	1.3255	0.035
39DAP/reference	1.07067	0.705
41DAP/reference	1.38257	0.012
42DAP/reference	1.20965	0.233
43DAP/reference	1.40564	0.045
47DAP/reference	0.99034	0.671
52DAP/reference	1.26904	0.018
57DAP/reference	1.12687	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00658	0.952
17DAP/reference	0.98324	0.576
27DAP/reference	0.95639	0.452
39DAP/reference	0.80502	0.055
41DAP/reference	0.89676	0.137
42DAP/reference	1.14221	0.794
43DAP/reference	0.89672	0.236
47DAP/reference	1.05937	0.24
52DAP/reference	0.8562	0.005
57DAP/reference	1.21519	0.98

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02144	0.984
17DAP/reference	1.07155	0.685
27DAP/reference	1.03997	0.834
39DAP/reference	1.18856	0.094
41DAP/reference	1.08969	0.889
42DAP/reference	0.93465	0.287
43DAP/reference	0.93726	0.365
47DAP/reference	0.94055	0.306
52DAP/reference	1.25865	0.19
57DAP/reference	1.05398	0.648

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00079	1
26DAP/20DAP	1.08814	0.635
34DAP/26DAP	0.97644	0.92
51DAP/34DAP	1.09293	0.271
52DAP/51DAP	1.0623	0.238
53DAP/52DAP	0.96251	0.824
55DAP/53DAP	0.91742	0.544
57DAP/55DAP	0.92785	0.652
62DAP/57DAP	0.93066	0.466
68DAP/62DAP	1.07924	0.912
68DAP/14DAP	1.02888	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21284	0.039

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.16897	0.058
Mature Green Tomato/Ripe Tomato	0.45759	0.019
Immature Eggplant/Mature Eggplant	0.99421	1
Ripe Pepper/Ripe Tomato	0.37217	0.224
Mature Eggplant/Ripe Tomato	0.57117	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01983	0.591
1-1-2/M82	1.0345	1
12-2/M82	1.10617	1
12-4/M82	1.02988	1
1-3/M82	1.23619	0.248
2-1-1/M82	0.9357	0.465
2-1/M82	N/A	N/A
2-6/M82	0.96948	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.99096	1
4-1/M82	1.24155
4-3-2/M82	1.02729	1
4-3/M82	1.17783	1
5-3/M82	1.07084	1
6-2/M82	1.00815	1
6-3/M82	0.97302	1
7-1/M82	0.97323	1
7-2/M82	1.139	1
9-3-2/M82	1.14425

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12288	0.493
IL2-6/WTpooled	0.65986	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12082	1
IL12-4/WTpooled	0.92972	0.71
IL1-4/WTpooled	0.77794
WT/WTpooled	1.05502	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	1.00488	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07347	0.774
DC3000/delta hrp 6h	1.26334	0.95
DC3000/delta hrp 12h	1.01478	1
DC3000/delta hrp 24h	1.05339	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13631	0.057
DC3000 delta B/DC3000 delta AB	1.17191	0.2

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04423	1
Exp 36h	1.71841	0.349
Exp 60h	2.05687	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97783	1
Var 0h	1.94044	0.421
Var 12h I row2-row1	1.36276	0.473
Var 12h NI row2-row1	1.14615	0.649
Var 36h I row2-row1	1.19035	0.601
Var 36h NI row2-row1	0.88749	0.432
Var 60h I row2-row1	0.81127	0.439
Var 60h NI row2-row1	0.9533	1
Time course 0hI-0hNI	0.94744	0.485
Time course 12hI-12hNI	1.09064	0.237
Time course 36hI-36hNI	1.64345	0.004
Time course 60hI-60hNI	6.53951	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)	1.0814	0.297
transgenic ySAMdc/azygous control (breaker)	1.26437	1
transgenic ySAMdc/azygous control (red)	1.15057	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01372	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.53016	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23166	0.096
Manapal/WT (break)	1.17687	1
Manapal/WT (red)	1.00957	1