Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.3.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07834	0.863
27DAP/17DAP	1.17757	0.839
39DAP/27DAP	1.8784	0.088
41DAP/39DAP	0.74388	0.147
42DAP/41DAP	1.13072	0.856
43DAP/42DAP	1.04583	1
47DAP/43DAP	1.09267	0.776
52DAP/47DAP	1.12954	0.767
57DAP/52DAP	1.43297	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62658	0.028
17DAP/reference	0.64853	0.007
27DAP/reference	0.78209	0.428
39DAP/reference	0.56007	0.02
41DAP/reference	0.54613	0.008
42DAP/reference	0.74114	0.004
43DAP/reference	0.60781	0.259
47DAP/reference	0.83557	0.042
52DAP/reference	1.39001	0.018
57DAP/reference	0.74456	0.235

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49476	0.043
27DAP/17DAP	1.09251	0.593
39DAP/27DAP	1.01049	0.862
41DAP/39DAP	1.15819	0.799
42DAP/41DAP	1.13656	0.308
43DAP/42DAP	0.89086	0.172
47DAP/43DAP	1.02912	0.873
52DAP/47DAP	0.9488	0.839
57DAP/52DAP	1.17762	0.234
57DAP/7DAP	1.49158	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35501	0.126
17DAP/reference	1.51275	0.007
27DAP/reference	1.28387	0.018
39DAP/reference	1.78985	0.007
41DAP/reference	1.48145	0.015
42DAP/reference	1.64171	0.008
43DAP/reference	1.93415	0.007
47DAP/reference	1.3308	0.121
52DAP/reference	1.69628	0.015
57DAP/reference	1.73132	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78499	0.037
17DAP/reference	0.76972	0.008
27DAP/reference	0.92276	0.257
39DAP/reference	1.13231	0.335
41DAP/reference	0.96146	0.403
42DAP/reference	1.01689	1
43DAP/reference	0.71506	0.031
47DAP/reference	0.90405	0.023
52DAP/reference	0.94375	0.203
57DAP/reference	0.75576	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40563	0.046
17DAP/reference	0.96569	0.601
27DAP/reference	1.49255	0.021
39DAP/reference	1.36183	0.03
41DAP/reference	1.42311	0.024
42DAP/reference	1.38153	0.03
43DAP/reference	1.31581	0.026
47DAP/reference	0.97573	0.509
52DAP/reference	1.46046	0.058
57DAP/reference	1.9039	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.58871	0.966
26DAP/20DAP	1.39046	0.273
34DAP/26DAP	0.75632	0.498
51DAP/34DAP	1.35018	0.055
52DAP/51DAP	0.86711	1
53DAP/52DAP	1.18795	0.196
55DAP/53DAP	0.84482	0.135
57DAP/55DAP	1.02588	0.904
62DAP/57DAP	0.8345	0.466
68DAP/62DAP	2.32409	0.029
68DAP/14DAP	3.19464	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38026	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.66155	0.167
Mature Green Tomato/Ripe Tomato	0.86554	0.051
Immature Eggplant/Mature Eggplant	1.3854	0.13
Ripe Pepper/Ripe Tomato	0.82277	0.224
Mature Eggplant/Ripe Tomato	0.41295	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84592	0.907
1-1-2/M82	1.28503	1
12-2/M82	0.91125	0.955
12-4/M82	0.89316	1
1-3/M82	1.46636	0.479
2-1-1/M82	1.1086	0.342
2-1/M82	0.9081	1
2-6/M82	0.92209	1
3-2/M82	1.11728	0.717
4-1-1/M82	0.96477	1
4-1/M82	0.98266	1
4-3-2/M82	0.8932	1
4-3/M82	1.19398	1
5-3/M82	1.50589	0.572
6-2/M82	0.98147	1
6-3/M82	0.935	1
7-1/M82	0.97568	1
7-2/M82	1.09644	1
9-3-2/M82	1.04533	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.29809
IL2-6/WTpooled	1.0761	1
IL7-5/WTpooled	1.39213
IL7-3/WTpooled	2.70948	1
IL12-4/WTpooled	1.11194	1
IL1-4/WTpooled	4.32024	1
WT/WTpooled	0.90679	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	1.10563	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06238	0.914
DC3000/delta hrp 6h	1.19105	1
DC3000/delta hrp 12h	0.94081	1
DC3000/delta hrp 24h	1.07476	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01395	1
DC3000 delta B/DC3000 delta AB	1.09417	0.386

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13351	1
Exp 36h	N/A	N/A
Exp 60h	1.32644	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93187	1
Var 0h	1.106	0.259
Var 12h I row2-row1	0.92147	0.514
Var 12h NI row2-row1	1.26757	0.649
Var 36h I row2-row1	0.96133	1
Var 36h NI row2-row1	0.84388	0.549
Var 60h I row2-row1	0.84072	0.306
Var 60h NI row2-row1	0.90027	0.516
Time course 0hI-0hNI	0.93428	0.56
Time course 12hI-12hNI	1.01179	0.888
Time course 36hI-36hNI	1.33499	0.006
Time course 60hI-60hNI	2.31435	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)	1.0076	1
transgenic ySAMdc/azygous control (breaker)	0.83217	0.251
transgenic ySAMdc/azygous control (red)	1.05657	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.19347	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68693	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71106	1
Manapal/WT (break)	0.97091	1
Manapal/WT (red)	1.04565	1