Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05016	0.975
27DAP/17DAP	0.87335	0.749
39DAP/27DAP	1.17562	0.91
41DAP/39DAP	0.87692	0.597
42DAP/41DAP	0.74039	0.774
43DAP/42DAP	0.84493	0.7
47DAP/43DAP	0.9517	0.724
52DAP/47DAP	1.21234	0.601
57DAP/52DAP	1.00192	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93584	0.352
17DAP/reference	1.01706	1
27DAP/reference	1.16595	0.165
39DAP/reference	1.06558	0.593
41DAP/reference	1.20399	0.058
42DAP/reference	0.9302	0.12
43DAP/reference	0.99712	0.904
47DAP/reference	1.04959	0.685
52DAP/reference	1.02755	1
57DAP/reference	1.12638	0.173

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.38197	0.053
27DAP/17DAP	1.22894	0.258
39DAP/27DAP	1.31339	0.079
41DAP/39DAP	1.14277	0.304
42DAP/41DAP	0.85717	0.123
43DAP/42DAP	1.24829	0.056
47DAP/43DAP	1.00841	0.973
52DAP/47DAP	1.08612	0.713
57DAP/52DAP	0.83231	0.098
57DAP/7DAP	1.79159	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88436	0.168
17DAP/reference	0.99228	0.599
27DAP/reference	1.1134	0.107
39DAP/reference	1.03136	0.745
41DAP/reference	1.10069	0.491
42DAP/reference	1.19906	0.1
43DAP/reference	1.03597	1
47DAP/reference	1.06263	0.647
52DAP/reference	1.03448	1
57DAP/reference	1.02528	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19028	0.049
17DAP/reference	1.02877	1
27DAP/reference	1.06384	0.715
39DAP/reference	1.32407	0.011
41DAP/reference	0.96672	0.188
42DAP/reference	1.02468	1
43DAP/reference	1.67919	0.022
47DAP/reference	1.20447	0.017
52DAP/reference	1.30626	0.208
57DAP/reference	1.3376	0.08

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90601	0.23
17DAP/reference	0.93359	0.407
27DAP/reference	1.03894	0.695
39DAP/reference	1.12599	0.048
41DAP/reference	1.08063	0.57
42DAP/reference	1.06294	0.635
43DAP/reference	0.98525	0.712
47DAP/reference	0.95343	0.465
52DAP/reference	1.14595	0.566
57DAP/reference	1.13832	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14779	0.966
26DAP/20DAP	0.95389	1
34DAP/26DAP	1.00155	1
51DAP/34DAP	0.76373	0.079
52DAP/51DAP	0.845	0.151
53DAP/52DAP	1.18332	0.162
55DAP/53DAP	1.00349	0.951
57DAP/55DAP	1.0185	1
62DAP/57DAP	1.07049	0.833
68DAP/62DAP	1.18324	0.792
68DAP/14DAP	1.29657

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.99255	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.62879	0.189
Mature Green Tomato/Ripe Tomato	0.91745	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.01372	1
Mature Eggplant/Ripe Tomato	0.43238	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95852	0.961
1-1-2/M82	1.20891
12-2/M82	N/A	N/A
12-4/M82	0.84199	0.319
1-3/M82	0.84007	0.501
2-1-1/M82	0.69943
2-1/M82	0.56665
2-6/M82	1.2664	0.695
3-2/M82	0.98773
4-1-1/M82	N/A	N/A
4-1/M82	1.29598
4-3-2/M82	0.56472
4-3/M82	0.61458	0.611
5-3/M82	1.01002	1
6-2/M82	1.05185
6-3/M82	0.95991	1
7-1/M82	N/A	N/A
7-2/M82	1.33528
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19288	0.365
IL2-6/WTpooled	0.81223	1
IL7-5/WTpooled	0.87572	1
IL7-3/WTpooled	1.27473	1
IL12-4/WTpooled	0.92235	0.71
IL1-4/WTpooled	0.90678	0.476
WT/WTpooled	0.97693	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	0.95583	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02951	0.921
DC3000/delta hrp 6h	1.71962	1
DC3000/delta hrp 12h	1.16492	1
DC3000/delta hrp 24h	1.02033	0.797

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	1.2847	0.468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07432	1
Exp 36h	1.57939	0.489
Exp 60h	1.22724	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98012	1
Var 0h	0.97945	1
Var 12h I row2-row1	1.13904	0.58
Var 12h NI row2-row1	0.95944	0.627
Var 36h I row2-row1	1.01156	1
Var 36h NI row2-row1	0.84841	0.549
Var 60h I row2-row1	0.90345	0.285
Var 60h NI row2-row1	0.9619	1
Time course 0hI-0hNI	1.00369	1
Time course 12hI-12hNI	1.08185	0.445
Time course 36hI-36hNI	1.27425	0.056
Time course 60hI-60hNI	1.94158	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)	1.0542	0.431
transgenic ySAMdc/azygous control (breaker)	0.92573	0.49
transgenic ySAMdc/azygous control (red)	0.94472	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01102	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77095	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91619	1
Manapal/WT (break)	0.80713	0.333
Manapal/WT (red)	1.08682	1