Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.2.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0715	0.977
27DAP/17DAP	1.2667	0.839
39DAP/27DAP	0.74651	0.443
41DAP/39DAP	0.97752	0.89
42DAP/41DAP	0.8196	0.774
43DAP/42DAP	1.07643	1
47DAP/43DAP	1.54781	0.216
52DAP/47DAP	1.04809	0.93
57DAP/52DAP	1.35122	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90443	0.262
17DAP/reference	0.76231	0.169
27DAP/reference	0.9499	0.61
39DAP/reference	1.02241	0.975
41DAP/reference	0.8214	0.016
42DAP/reference	0.92599	0.139
43DAP/reference	1.13246	N/A
47DAP/reference	1.16837	0.391
52DAP/reference	1.63567	0.242
57DAP/reference	2.30653	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85027	0.484
27DAP/17DAP	1.0978	0.735
39DAP/27DAP	1.02954	1
41DAP/39DAP	0.9567	0.934
42DAP/41DAP	1.0266	0.924
43DAP/42DAP	1.19173	0.042
47DAP/43DAP	1.25112	0.344
52DAP/47DAP	1.17043	0.799
57DAP/52DAP	0.90119	0.551
57DAP/7DAP	0.92476	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12677	0.452
17DAP/reference	1.62387	0.199
27DAP/reference	1.24507	0.246
39DAP/reference	1.18589	0.175
41DAP/reference	0.97027	0.469
42DAP/reference	1.1063	0.308
43DAP/reference	1.21958	0.289
47DAP/reference	1.0365	1
52DAP/reference	1.25867	0.105
57DAP/reference	1.13898	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08828	0.802
17DAP/reference	0.89691	0.279
27DAP/reference	0.93883	0.407
39DAP/reference	0.97998	0.569
41DAP/reference	0.97325	0.472
42DAP/reference	0.87726	0.098
43DAP/reference	0.81401	0.095
47DAP/reference	0.80232	0.014
52DAP/reference	0.97678	0.537
57DAP/reference	0.89014	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82925	0.183
17DAP/reference	0.94542	0.571
27DAP/reference	1.15828	0.695
39DAP/reference	1.00439	0.889
41DAP/reference	0.81754	0.107
42DAP/reference	1.20952	0.716
43DAP/reference	0.76185	0.032
47DAP/reference	1.00266	0.731
52DAP/reference	0.96451	0.704
57DAP/reference	1.22179	0.285

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31783	1
26DAP/20DAP	1.14446	0.558
34DAP/26DAP	1.02741	0.98
51DAP/34DAP	1.14371	0.988
52DAP/51DAP	1.48565	0.271
53DAP/52DAP	0.82133	0.595
55DAP/53DAP	0.99225	0.886
57DAP/55DAP	0.95008	0.795
62DAP/57DAP	0.9571	0.994
68DAP/62DAP	0.8648	0.722
68DAP/14DAP	0.5889	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86945	0.145

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70804	0.272
Mature Green Tomato/Ripe Tomato	0.78559	0.148
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.59804	0.224
Mature Eggplant/Ripe Tomato	0.4737	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91892	N/A
1-1-2/M82	1.11849	N/A
12-2/M82	N/A	N/A
12-4/M82	0.94271	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.14281	1
5-3/M82	0.96317	0.642
6-2/M82	1.02227	1
6-3/M82	1.20527	1
7-1/M82	N/A	N/A
7-2/M82	1.17388	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.01437	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.79757	1
IL12-4/WTpooled	1.19712	0.839
IL1-4/WTpooled	0.89489	0.699
WT/WTpooled	1.02404	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	0.92691	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96406	1
DC3000/delta hrp 6h	0.92248	0.95
DC3000/delta hrp 12h	0.99279	1
DC3000/delta hrp 24h	0.95998	0.818

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94065	1
Exp 36h	1.34385	0.326
Exp 60h	1.15624	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.19913	N/A
Var 0h	1.12479	0.936
Var 12h I row2-row1	1.09513	0.163
Var 12h NI row2-row1	1.14835	1
Var 36h I row2-row1	1.1986	0.742
Var 36h NI row2-row1	1.13966	N/A
Var 60h I row2-row1	0.92767	0.952
Var 60h NI row2-row1	0.98767	1
Time course 0hI-0hNI	0.95964	0.781
Time course 12hI-12hNI	1.06447	0.633
Time course 36hI-36hNI	1.1141	0.316
Time course 60hI-60hNI	1.11786	0.096

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)	0.91837	0.33
transgenic ySAMdc/azygous control (breaker)	1.04759	1
transgenic ySAMdc/azygous control (red)	0.93155	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01828	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97873	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96183	1
Manapal/WT (break)	0.8335	0.333
Manapal/WT (red)	0.99722	1