Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.13.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83526	0.303
27DAP/17DAP	1.1746	0.845
39DAP/27DAP	1.41861	0.215
41DAP/39DAP	1.03818	0.958
42DAP/41DAP	0.84541	1
43DAP/42DAP	0.88368	0.801
47DAP/43DAP	1.04141	0.744
52DAP/47DAP	1.62172	0.273
57DAP/52DAP	0.78369	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06165	0.5
17DAP/reference	0.90914	0.104
27DAP/reference	0.9244	0.141
39DAP/reference	0.87388	0.194
41DAP/reference	0.80079	0.021
42DAP/reference	1.28403	0.007
43DAP/reference	0.8761	0.123
47DAP/reference	0.88159	0.055
52DAP/reference	0.97334	0.489
57DAP/reference	1.01252	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01945	0.801
27DAP/17DAP	0.983	0.919
39DAP/27DAP	1.07976	0.603
41DAP/39DAP	1.11512	0.612
42DAP/41DAP	0.90317	0.429
43DAP/42DAP	0.92811	0.246
47DAP/43DAP	1.06382	0.889
52DAP/47DAP	2.06072	0.045
57DAP/52DAP	3.13086	0.029
57DAP/7DAP	1.65279	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07232	0.545
17DAP/reference	1.09579	0.328
27DAP/reference	1.09371	0.301
39DAP/reference	1.92748	0.008
41DAP/reference	1.39244	0.016
42DAP/reference	1.79048	0.007
43DAP/reference	2.23086	0.007
47DAP/reference	1.18349	0.068
52DAP/reference	1.68905	0.011
57DAP/reference	1.9609	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90705	0.277
17DAP/reference	1.108	0.471
27DAP/reference	0.942	0.366
39DAP/reference	1.20322	0.141
41DAP/reference	1.06342	0.925
42DAP/reference	0.85876	0.05
43DAP/reference	0.97667	0.62
47DAP/reference	0.87807	0.099
52DAP/reference	0.92648	0.131
57DAP/reference	0.78481	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87138	0.127
17DAP/reference	0.86004	0.165
27DAP/reference	1.26211	0.03
39DAP/reference	1.03825	0.792
41DAP/reference	1.03048	0.889
42DAP/reference	1.04417	0.68
43DAP/reference	1.10153	0.547
47DAP/reference	0.73847	0.021
52DAP/reference	1.04724	0.801
57DAP/reference	0.79271	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94204	1
26DAP/20DAP	0.9645	0.156
34DAP/26DAP	1.0692	1
51DAP/34DAP	1.1925	0.957
52DAP/51DAP	1.2732	0.51
53DAP/52DAP	1.21688
55DAP/53DAP	1.40724	0.584
57DAP/55DAP	0.7738	0.268
62DAP/57DAP	0.89864	0.681
68DAP/62DAP	1.52772	0.872
68DAP/14DAP	1.29492	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.41253	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.98513	0.835
Immature Eggplant/Mature Eggplant	0.55648	0.086
Ripe Pepper/Ripe Tomato	0.04564	0.224
Mature Eggplant/Ripe Tomato	0.22006	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89745	0.944
1-1-2/M82	0.95934	1
12-2/M82	4.04584	1
12-4/M82	0.85896	0.619
1-3/M82	1.05344	0.479
2-1-1/M82	0.95835	1
2-1/M82	1.31828	1
2-6/M82	0.87336	1
3-2/M82	0.929
4-1-1/M82	0.77525	0.883
4-1/M82	1.05296
4-3-2/M82	1.24698
4-3/M82	1.12837	1
5-3/M82	0.6314	0.419
6-2/M82	1.49974	0.235
6-3/M82	1.13906	1
7-1/M82	0.89104	0.509
7-2/M82	0.78112	0.486
9-3-2/M82	0.87019	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.68087	0.337
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.32251	1
IL12-4/WTpooled	1.36238	0.516
IL1-4/WTpooled	1.02482	1
WT/WTpooled	0.98395	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	0.86945	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14701	0.921
DC3000/delta hrp 6h	1.01653	0.95
DC3000/delta hrp 12h	0.73894	1
DC3000/delta hrp 24h	3.5477	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32395	0.052
DC3000 delta B/DC3000 delta AB	1.21996	0.201

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94148	1
Exp 36h	0.7015	0.406
Exp 60h	0.78242	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99644	1
Var 0h	0.89985	1
Var 12h I row2-row1	0.74688	0.514
Var 12h NI row2-row1	1.30875	0.649
Var 36h I row2-row1	0.8622	1
Var 36h NI row2-row1	2.18499	1
Var 60h I row2-row1	0.77074	0.285
Var 60h NI row2-row1	1.05649	1
Time course 0hI-0hNI	1.07166	0.764
Time course 12hI-12hNI	0.79553	0.042
Time course 36hI-36hNI	0.461	0.023
Time course 60hI-60hNI	2.92442	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)	1.48973	0.297
transgenic ySAMdc/azygous control (breaker)	0.80775	0.173
transgenic ySAMdc/azygous control (red)	1.20274	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01882	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18618	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.49621	0.172
Manapal/WT (break)	1.03547	1
Manapal/WT (red)	0.4298	0.181