Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83442	0.331
27DAP/17DAP	0.8373	0.577
39DAP/27DAP	1.04447	1
41DAP/39DAP	0.94484	0.849
42DAP/41DAP	0.7661	0.774
43DAP/42DAP	1.13538	0.894
47DAP/43DAP	0.80851	0.386
52DAP/47DAP	1.27845	0.69
57DAP/52DAP	1.0798	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81433	0.083
17DAP/reference	0.77186	0.043
27DAP/reference	0.83013	0.201
39DAP/reference	0.82899	0.24
41DAP/reference	0.69506	0.026
42DAP/reference	0.724	0.032
43DAP/reference	0.99793
47DAP/reference	1.10726	0.674
52DAP/reference	1.25041	0.05
57DAP/reference	1.08694	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18242	0.558
27DAP/17DAP	1.51039	0.22
39DAP/27DAP	1.1753	0.534
41DAP/39DAP	0.80859	0.63
42DAP/41DAP	1.12179	0.727
43DAP/42DAP	1.05536	0.699
47DAP/43DAP	0.99797	0.989
52DAP/47DAP	1.15872	0.689
57DAP/52DAP	1.24076	0.533
57DAP/7DAP	1.59046	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31636	0.056
17DAP/reference	1.18179	0.02
27DAP/reference	1.27752	0.041
39DAP/reference	1.49713	0.126
41DAP/reference	1.6522	0.021
42DAP/reference	1.1324	0.405
43DAP/reference	1.08831	0.637
47DAP/reference	1.05303	0.791
52DAP/reference	0.83473	0.126
57DAP/reference	0.97579	0.458

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08243	0.915
17DAP/reference	0.7547	0.016
27DAP/reference	0.86397	0.032
39DAP/reference	0.9177	0.126
41DAP/reference	0.8471	0.083
42DAP/reference	1.02567	1
43DAP/reference	0.90545	0.307
47DAP/reference	0.92086	0.188
52DAP/reference	0.92491	0.302
57DAP/reference	0.7792	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	6.15603	0.019
17DAP/reference	0.91491	0.328
27DAP/reference	1.53434	0.227
39DAP/reference	1.05088	0.578
41DAP/reference	1.08248	0.588
42DAP/reference	8.05883	0.016
43DAP/reference	4.87213	0.02
47DAP/reference	0.92659	0.315
52DAP/reference	6.95704	0.088
57DAP/reference	2.97333	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24834	0.586
26DAP/20DAP	1.90618
34DAP/26DAP	1.09498
51DAP/34DAP	1.92578	0.993
52DAP/51DAP	1.16628	0.808
53DAP/52DAP	1.34561	0.868
55DAP/53DAP	1.28751	0.082
57DAP/55DAP	1.07317	1
62DAP/57DAP	14.1276
68DAP/62DAP	1.31669
68DAP/14DAP	0.96158

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.63519	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.19652	0.026
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.80734
Mature Eggplant/Ripe Tomato	1.08029	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.84019	0.25
1-3/M82	1.04976
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.12929	0.374
3-2/M82	0.74185
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	0.97726
5-3/M82	1.04908
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.22526	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.07508	0.493
IL2-6/WTpooled	0.8631	0.473
IL7-5/WTpooled	0.90579	1
IL7-3/WTpooled	0.84214	1
IL12-4/WTpooled	1.09362	1
IL1-4/WTpooled	1.00915	1
WT/WTpooled	1.08523	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	1.11381	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99149	1
DC3000/delta hrp 6h	0.95564	0.95
DC3000/delta hrp 12h	1.16325	1
DC3000/delta hrp 24h	0.75533	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96373	0.724
DC3000 delta B/DC3000 delta AB	0.78165	0.152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04368	1
Exp 36h	1.2741	0.693
Exp 60h	1.29878	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98533	1
Var 0h	3.087	0.782
Var 12h I row2-row1	0.87725	0.357
Var 12h NI row2-row1	0.92103	0.713
Var 36h I row2-row1	0.92884	1
Var 36h NI row2-row1	1.45515	1
Var 60h I row2-row1	1.4677	0.562
Var 60h NI row2-row1	0.98932	1
Time course 0hI-0hNI	0.9751	0.879
Time course 12hI-12hNI	0.93722	0.458
Time course 36hI-36hNI	0.82375	0.023
Time course 60hI-60hNI	0.27353	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)	0.90372	0.314
transgenic ySAMdc/azygous control (breaker)	0.9003	0.15
transgenic ySAMdc/azygous control (red)	1.06686	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.45224	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.31018	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.51536	0.096
Manapal/WT (break)	1.17866	0.381
Manapal/WT (red)	1.07087	1