Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45684	0.219
27DAP/17DAP	0.6334	0.033
39DAP/27DAP	0.74877	0.392
41DAP/39DAP	0.83687	0.478
42DAP/41DAP	1.06513	1
43DAP/42DAP	1.11027	1
47DAP/43DAP	0.76518	0.321
52DAP/47DAP	1.23333	0.559
57DAP/52DAP	0.76121	0.506

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94976	0.39
17DAP/reference	1.05437	0.342
27DAP/reference	0.89072	0.286
39DAP/reference	0.79231	0.023
41DAP/reference	0.76953	0.01
42DAP/reference	0.76926	0.002
43DAP/reference	0.81492	0.155
47DAP/reference	0.85694	0.038
52DAP/reference	0.87656	0.131
57DAP/reference	1.05888	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72532	0.087
27DAP/17DAP	1.5061	0.117
39DAP/27DAP	0.43569	0.045
41DAP/39DAP	1.18928	0.801
42DAP/41DAP	1.02145	0.936
43DAP/42DAP	0.74877	0.032
47DAP/43DAP	0.95822	0.846
52DAP/47DAP	1.22999	0.619
57DAP/52DAP	1.20635	0.606
57DAP/7DAP	0.54055	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87475	0.037
17DAP/reference	1.21463	0.199
27DAP/reference	0.93377	0.231
39DAP/reference	0.98469	0.552
41DAP/reference	1.07419	0.375
42DAP/reference	0.91808	0.289
43DAP/reference	1.18772	0.83
47DAP/reference	0.88324	0.128
52DAP/reference	0.77908	0.053
57DAP/reference	0.8228	0.074

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07849	0.933
17DAP/reference	1.1081	0.873
27DAP/reference	1.26525	0.089
39DAP/reference	0.97073	0.485
41DAP/reference	0.87988	0.137
42DAP/reference	0.88192	0.055
43DAP/reference	0.7486	0.125
47DAP/reference	0.72823	0.018
52DAP/reference	0.90826	0.171
57DAP/reference	0.80111	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29818	0.103
17DAP/reference	1.19451	0.145
27DAP/reference	1.05563	0.271
39DAP/reference	1.025	0.733
41DAP/reference	0.86665	0.096
42DAP/reference	0.89536	0.287
43DAP/reference	0.78204	0.092
47DAP/reference	0.83835	0.023
52DAP/reference	0.73873	0.122
57DAP/reference	0.92017	0.273

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8715	1
26DAP/20DAP	1.42861	0.197
34DAP/26DAP	0.73028	0.294
51DAP/34DAP	0.95152	0.737
52DAP/51DAP	0.84713	1
53DAP/52DAP	0.99067	0.909
55DAP/53DAP	0.53368
57DAP/55DAP	0.65395	0.046
62DAP/57DAP	1.54883	0.115
68DAP/62DAP	1.04667	0.866
68DAP/14DAP	0.91339	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0439	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.88274	0.058
Mature Green Tomato/Ripe Tomato	4.36348	0.015
Immature Eggplant/Mature Eggplant	2.73984	0.05
Ripe Pepper/Ripe Tomato	2.61603	0.258
Mature Eggplant/Ripe Tomato	4.14179	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.72476	0.409
1-1-2/M82	0.96657	1
12-2/M82	1.073
12-4/M82	0.7638	0.358
1-3/M82	N/A	N/A
2-1-1/M82	1.04082
2-1/M82	N/A	N/A
2-6/M82	1.62437
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	1.68786	0.268
5-3/M82	0.93838	1
6-2/M82	N/A	N/A
6-3/M82	0.6189
7-1/M82	0.93655
7-2/M82	0.93473
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09811	0.493
IL2-6/WTpooled	1.08902	0.531
IL7-5/WTpooled	1.00088
IL7-3/WTpooled	1.17078	1
IL12-4/WTpooled	0.73655	0.581
IL1-4/WTpooled	0.99263	1
WT/WTpooled	0.96848	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	0.97563	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93465	1
DC3000/delta hrp 6h	1.26761	0.582
DC3000/delta hrp 12h	0.95024	1
DC3000/delta hrp 24h	0.80986	0.092

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53901	0.065
DC3000 delta B/DC3000 delta AB	0.44495	0.027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75611	1
Exp 36h	0.69456	0.434
Exp 60h	0.58662	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02134	1
Var 0h	1.03206	1
Var 12h I row2-row1	0.9853	1
Var 12h NI row2-row1	0.93135	0.627
Var 36h I row2-row1	0.97925	1
Var 36h NI row2-row1	1.09221	1
Var 60h I row2-row1	1.28394	0.543
Var 60h NI row2-row1	1.0719	0.904
Time course 0hI-0hNI	0.93237	0.618
Time course 12hI-12hNI	0.9634	0.739
Time course 36hI-36hNI	0.84251	0.054
Time course 60hI-60hNI	0.29873	0.005

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)	1.24773	0.272
transgenic ySAMdc/azygous control (breaker)	0.67825	0.251
transgenic ySAMdc/azygous control (red)	0.68177	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02274	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95236	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79869	1
Manapal/WT (break)	1.89756	0.123
Manapal/WT (red)	1.81062	0.15