Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85091	0.26
27DAP/17DAP	1.0838	0.866
39DAP/27DAP	0.97434	0.7
41DAP/39DAP	1.24297	0.54
42DAP/41DAP	0.97913	1
43DAP/42DAP	0.97889	0.925
47DAP/43DAP	1.00878	0.959
52DAP/47DAP	1.39549	0.418
57DAP/52DAP	0.82665	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76874	0.052
17DAP/reference	0.70234	0.022
27DAP/reference	0.88163	0.265
39DAP/reference	0.894	0.267
41DAP/reference	0.7168	0.114
42DAP/reference	0.81599	0.033
43DAP/reference	0.98281	0.728
47DAP/reference	0.80551	0.077
52DAP/reference	1.14276	0.766
57DAP/reference	0.99595	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87121	0.277
27DAP/17DAP	1.06552	0.686
39DAP/27DAP	0.96737	0.622
41DAP/39DAP	0.97561	0.959
42DAP/41DAP	0.97193	0.721
43DAP/42DAP	1.02486	0.627
47DAP/43DAP	1.05856	0.325
52DAP/47DAP	1.00907	0.979
57DAP/52DAP	1.13192	0.455
57DAP/7DAP	1.06184	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14536	0.481
17DAP/reference	1.24192	0.042
27DAP/reference	1.20285	0.131
39DAP/reference	1.44202	0.008
41DAP/reference	1.43591	0.104
42DAP/reference	1.65759	0.006
43DAP/reference	1.2048	0.079
47DAP/reference	1.03355	1
52DAP/reference	1.15425	0.139
57DAP/reference	1.13135	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79396	0.134
17DAP/reference	0.61736	0.008
27DAP/reference	0.75451	0.024
39DAP/reference	0.60705	0.025
41DAP/reference	0.82086	0.173
42DAP/reference	0.79896	0.037
43DAP/reference	0.69019	0.034
47DAP/reference	0.657	0.008
52DAP/reference	0.53534	0.003
57DAP/reference	0.42197	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21005	0.386
17DAP/reference	0.91409	0.444
27DAP/reference	1.04469	0.777
39DAP/reference	1.02059	0.889
41DAP/reference	1.1779	0.089
42DAP/reference	1.15149	0.364
43DAP/reference	1.01421	0.796
47DAP/reference	0.92802	0.348
52DAP/reference	0.86446	0.351
57DAP/reference	1.38969	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03966	0.966
26DAP/20DAP	1.07934	1
34DAP/26DAP	1.39382	0.542
51DAP/34DAP	0.96154	0.747
52DAP/51DAP	1.74914	0.037
53DAP/52DAP	0.91015	0.409
55DAP/53DAP	1.00429	0.876
57DAP/55DAP	0.86753	0.527
62DAP/57DAP	1.29195	0.393
68DAP/62DAP	1.36257	0.722
68DAP/14DAP	1.47285	0.594

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81312	0.224

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.79309	0.317
Immature Eggplant/Mature Eggplant	0.91229	0.407
Ripe Pepper/Ripe Tomato	0.15849	0.224
Mature Eggplant/Ripe Tomato	1.28857	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95166	0.961
1-1-2/M82	0.96225	1
12-2/M82	1.14715	0.61
12-4/M82	1.12422	1
1-3/M82	1.03239	1
2-1-1/M82	1.02528
2-1/M82	0.99314	0.74
2-6/M82	1.26127	0.695
3-2/M82	0.94825
4-1-1/M82	1.07169	1
4-1/M82	1.31441	0.512
4-3-2/M82	1.24129	0.508
4-3/M82	1.27825	0.268
5-3/M82	1.06095	1
6-2/M82	1.11313
6-3/M82	1.01656	1
7-1/M82	1.0331
7-2/M82	N/A	N/A
9-3-2/M82	0.99339	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95932
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.39901
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.14544	0.839
IL1-4/WTpooled	0.79714	0.834
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	1.30681	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09563	0.774
DC3000/delta hrp 6h	1.02585	1
DC3000/delta hrp 12h	0.99216	1
DC3000/delta hrp 24h	1.06696	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23168	0.073
DC3000 delta B/DC3000 delta AB	1.3813	0.132

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.40867	0.228
Exp 36h	1.61002	0.349
Exp 60h	1.91117	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.04493	0.98
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.97998	0.789
transgenic ySAMdc/azygous control (breaker)	0.88311	0.173
transgenic ySAMdc/azygous control (red)	1.19949	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07884	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85983	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.83097	0.087
Manapal/WT (break)	0.97625	1
Manapal/WT (red)	0.59039	0.181