Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97895	0.779
27DAP/17DAP	0.84655	0.593
39DAP/27DAP	1.23044	0.681
41DAP/39DAP	1.08569	1
42DAP/41DAP	1.1877	0.73
43DAP/42DAP	1.11346	0.999
47DAP/43DAP	0.87172	0.584
52DAP/47DAP	0.93329	0.793
57DAP/52DAP	0.80507	0.687

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81892	0.101
17DAP/reference	1.1469	0.258
27DAP/reference	0.92904	0.17
39DAP/reference	1.00237	0.816
41DAP/reference	0.79565	0.018
42DAP/reference	0.81737	0.009
43DAP/reference	1.32175	0.074
47DAP/reference	0.94598	0.322
52DAP/reference	0.91431	0.223
57DAP/reference	1.07097	0.704

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02052	1
27DAP/17DAP	0.7958	0.121
39DAP/27DAP	0.77317	0.106
41DAP/39DAP	0.9351	0.696
42DAP/41DAP	0.97068	0.776
43DAP/42DAP	0.91711	0.367
47DAP/43DAP	0.96223	0.805
52DAP/47DAP	1.1845	0.573
57DAP/52DAP	1.02088	1
57DAP/7DAP	0.71502	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12261	0.344
17DAP/reference	1.27008	0.477
27DAP/reference	0.77488	0.264
39DAP/reference	1.13059	0.601
41DAP/reference	1.29435	0.291
42DAP/reference	1.47186	0.03
43DAP/reference	1.35405	0.432
47DAP/reference	1.148	0.241
52DAP/reference	1.18496	0.286
57DAP/reference	1.32697	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88026	0.119
17DAP/reference	0.79233	0.015
27DAP/reference	0.87845	0.269
39DAP/reference	0.83237	0.079
41DAP/reference	0.95877	0.373
42DAP/reference	0.95921	0.433
43DAP/reference	0.79043	0.044
47DAP/reference	1.07843	0.482
52DAP/reference	0.98574	0.537
57DAP/reference	1.0531	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92248	0.422
17DAP/reference	0.90601	0.508
27DAP/reference	0.7554	0.357
39DAP/reference	1.1139	0.235
41DAP/reference	0.72497
42DAP/reference	0.91836	0.671
43DAP/reference	0.90805	0.416
47DAP/reference	0.91525	0.269
52DAP/reference	0.94282	0.573
57DAP/reference	1.10338	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18737	0.916
26DAP/20DAP	0.77366	0.512
34DAP/26DAP	0.89958	0.834
51DAP/34DAP	1.79936	0.326
52DAP/51DAP	0.97342	1
53DAP/52DAP	0.83944	0.581
55DAP/53DAP	1.04831	0.939
57DAP/55DAP	1.03416	0.935
62DAP/57DAP	1.19257	0.868
68DAP/62DAP	1.47089	0.31
68DAP/14DAP	1.4965	0.125

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.38463	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.88894	0.411
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95616	0.944
1-1-2/M82	0.87686	0.958
12-2/M82	1.07806	1
12-4/M82	1.14862	1
1-3/M82	0.61795
2-1-1/M82	1.27463
2-1/M82	N/A	N/A
2-6/M82	1.11029	0.594
3-2/M82	0.79306	0.428
4-1-1/M82	1.19813	1
4-1/M82	1.17434	1
4-3-2/M82	1.14624	0.246
4-3/M82	0.89493	1
5-3/M82	0.93666	1
6-2/M82	0.81952	0.481
6-3/M82	1.04093	1
7-1/M82	1.16908	1
7-2/M82	0.87544	0.881
9-3-2/M82	1.06832	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85226	0.243
IL2-6/WTpooled	1.21465	0.788
IL7-5/WTpooled	1.17887	0.792
IL7-3/WTpooled	0.94164	1
IL12-4/WTpooled	1.24142	0.557
IL1-4/WTpooled	0.82393	0.435
WT/WTpooled	1.07472	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	0.88494	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05092	0.692
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.89553	1
DC3000/delta hrp 24h	1.08293	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44775	0.025
DC3000 delta B/DC3000 delta AB	0.39778	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83908	1
Exp 36h	0.99676	1
Exp 60h	0.86267	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96688	1
Var 0h	3.25257	0.936
Var 12h I row2-row1	0.74424	0.338
Var 12h NI row2-row1	0.89371	0.488
Var 36h I row2-row1	0.92874	1
Var 36h NI row2-row1	1.28364	1
Var 60h I row2-row1	1.29624	0.543
Var 60h NI row2-row1	0.92741	1
Time course 0hI-0hNI	0.94701	0.656
Time course 12hI-12hNI	0.99404	1
Time course 36hI-36hNI	0.8256	0.108
Time course 60hI-60hNI	0.23738	0.006

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)	0.98947	0.862
transgenic ySAMdc/azygous control (breaker)	0.9955	1
transgenic ySAMdc/azygous control (red)	0.95503	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94794	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.65336	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78195	0.172
Manapal/WT (break)	1.28089	0.183
Manapal/WT (red)	0.80754	0.503