Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6354	0.119
27DAP/17DAP	1.08837	0.868
39DAP/27DAP	1.13702	0.74
41DAP/39DAP	1.37693	0.372
42DAP/41DAP	1.12797	0.938
43DAP/42DAP	1.3096	0.527
47DAP/43DAP	1.61516	0.213
52DAP/47DAP	1.76524	0.11
57DAP/52DAP	0.70876	0.588

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21893	0.17
17DAP/reference	0.68901	0.009
27DAP/reference	0.80306	0.257
39DAP/reference	0.60376	0.009
41DAP/reference	0.52545	0.341
42DAP/reference	1.8568	0.001
43DAP/reference	1.33797
47DAP/reference	0.93495	0.445
52DAP/reference	1.27002	0.453
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07057	0.87
27DAP/17DAP	0.99175	0.943
39DAP/27DAP	0.82881	0.54
41DAP/39DAP	1.09806	0.861
42DAP/41DAP	0.76275	0.109
43DAP/42DAP	1.55965	0.031
47DAP/43DAP	1.39963	0.04
52DAP/47DAP	1.31534	0.293
57DAP/52DAP	5.17377	0.027
57DAP/7DAP	3.30164	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88703	0.08
17DAP/reference	0.76241	0.012
27DAP/reference	0.76739	0.013
39DAP/reference	0.72297	0.013
41DAP/reference	0.75722	0.017
42DAP/reference	0.95457	0.371
43DAP/reference	1.95165	0.012
47DAP/reference	0.97952	0.671
52DAP/reference	1.1187	0.599
57DAP/reference	1.25032	0.331

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98767	0.756
17DAP/reference	0.95513	0.41
27DAP/reference	1.18806	0.212
39DAP/reference	1.3101	0.077
41DAP/reference	1.11185	0.573
42DAP/reference	1.1729	0.342
43DAP/reference	0.84831	0.084
47DAP/reference	1.04431	1
52DAP/reference	0.89123	0.093
57DAP/reference	1.22093	0.03

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84265	0.077
17DAP/reference	0.76612	0.125
27DAP/reference	0.86212	0.067
39DAP/reference	0.79313	0.016
41DAP/reference	0.67451	0.018
42DAP/reference	1.05678	0.51
43DAP/reference	1.61866	0.024
47DAP/reference	1.79605	0.007
52DAP/reference	2.81336	0.027
57DAP/reference	2.96464	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2528	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	8.96913
51DAP/34DAP	0.4186
52DAP/51DAP	0.88053	1
53DAP/52DAP	0.93191	0.741
55DAP/53DAP	1.16771	0.911
57DAP/55DAP	7.6395	0.793
62DAP/57DAP	0.96245	0.994
68DAP/62DAP	1.50932	0.206
68DAP/14DAP	2.67306	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.4307	0.099

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.88709	1
Mature Green Tomato/Ripe Tomato	0.07966
Immature Eggplant/Mature Eggplant	1.64444	0.063
Ripe Pepper/Ripe Tomato	0.06927	0.224
Mature Eggplant/Ripe Tomato	0.24843	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0835	1
1-1-2/M82	1.02913	0.977
12-2/M82	1.05623	1
12-4/M82	1.02987	1
1-3/M82	1.21519	0.479
2-1-1/M82	1.09816	0.764
2-1/M82	1.05407	1
2-6/M82	1.20615	0.594
3-2/M82	1.00947	1
4-1-1/M82	1.04215	0.977
4-1/M82	1.11732	1
4-3-2/M82	1.13802	0.508
4-3/M82	1.09773	1
5-3/M82	0.75741	0.447
6-2/M82	1.00449
6-3/M82	0.81088	0.715
7-1/M82	0.9631	1
7-2/M82	1.06319	1
9-3-2/M82	1.17221	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03345	1
IL2-6/WTpooled	0.87344	1
IL7-5/WTpooled	0.63344
IL7-3/WTpooled	0.8963	0.418
IL12-4/WTpooled	1.02286	0.891
IL1-4/WTpooled	0.97668	1
WT/WTpooled	0.96897	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	0.90135	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99158	1
DC3000/delta hrp 6h	1.44573	1
DC3000/delta hrp 12h	1.01852	1
DC3000/delta hrp 24h	1.10613	0.673

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	0.85305

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17515	0.227
Exp 36h	1.04401	1
Exp 60h	0.87377	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96085	1
Var 0h	1.32225	0.421
Var 12h I row2-row1	1.22181	0.263
Var 12h NI row2-row1	0.96691	1
Var 36h I row2-row1	1.77104	0.908
Var 36h NI row2-row1	1.42028	1
Var 60h I row2-row1	1.06207
Var 60h NI row2-row1	0.83698	0.866
Time course 0hI-0hNI	0.95097	0.692
Time course 12hI-12hNI	0.92563	0.569
Time course 36hI-36hNI	1.47726	0.023
Time course 60hI-60hNI	0.6483	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)	1.53507	0.312
transgenic ySAMdc/azygous control (breaker)	0.47485	0.15
transgenic ySAMdc/azygous control (red)	1.05551	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05917	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0863	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11514	1
Manapal/WT (break)	1.14248	0.381
Manapal/WT (red)	0.87093	0.36