Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.20.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.49702	0.019
27DAP/17DAP	1.15665	0.845
39DAP/27DAP	2.05466	0.064
41DAP/39DAP	1.00234	0.915
42DAP/41DAP	1.28635	0.632
43DAP/42DAP	1.11907	0.968
47DAP/43DAP	0.76398	0.314
52DAP/47DAP	0.5399	0.061
57DAP/52DAP	1.27828	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.3823	0.024
17DAP/reference	1.10624	0.874
27DAP/reference	1.35923	0.011
39DAP/reference	0.88584	0.455
41DAP/reference	1.05445	0.624
42DAP/reference	1.19583	0.011
43DAP/reference	0.99875	0.924
47DAP/reference	0.94573	0.191
52DAP/reference	1.49678	0.011
57DAP/reference	1.2614	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	4.79316	0.036
27DAP/17DAP	0.77561	0.537
39DAP/27DAP	2.26872	0.095
41DAP/39DAP	0.80572	0.412
42DAP/41DAP	1.43211	0.193
43DAP/42DAP	1.27672	0.25
47DAP/43DAP	1.03798	1
52DAP/47DAP	0.9941	0.919
57DAP/52DAP	0.8009	0.203
57DAP/7DAP	2.52176	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8195	0.086
17DAP/reference	0.79184	0.011
27DAP/reference	0.67736	0.01
39DAP/reference	0.77518	0.011
41DAP/reference	0.77645	0.017
42DAP/reference	0.7088	0.01
43DAP/reference	0.71909	0.011
47DAP/reference	1.94663	0.187
52DAP/reference	0.79526	0.035
57DAP/reference	0.86069	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47218	0.026
17DAP/reference	0.68041	0.03
27DAP/reference	0.9342	0.467
39DAP/reference	1.30596	0.119
41DAP/reference	0.92761	0.173
42DAP/reference	1.0249	1
43DAP/reference	0.87895	0.292
47DAP/reference	1.2753	0.301
52DAP/reference	0.87922	0.06
57DAP/reference	1.26063	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75689	0.033
17DAP/reference	0.76434	0.144
27DAP/reference	0.71548	0.025
39DAP/reference	0.66968	0.007
41DAP/reference	0.77868	0.018
42DAP/reference	0.67494	0.019
43DAP/reference	0.80621	0.016
47DAP/reference	0.48826	0.005
52DAP/reference	0.60842	0.064
57DAP/reference	1.07896	0.892

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.834	0.65
26DAP/20DAP	1.06017	1
34DAP/26DAP	0.71108	0.234
51DAP/34DAP	1.70385	0.041
52DAP/51DAP	0.59002	0.151
53DAP/52DAP	1.24274	0.125
55DAP/53DAP	0.48619	0.021
57DAP/55DAP	0.79461	0.38
62DAP/57DAP	5.9295	0.002
68DAP/62DAP	1.78337	0.646
68DAP/14DAP	2.28838	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.81505	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72129	0.199
Mature Green Tomato/Ripe Tomato	1.5402	0.015
Immature Eggplant/Mature Eggplant	1.67754	0.05
Ripe Pepper/Ripe Tomato	2.09163	0.256
Mature Eggplant/Ripe Tomato	2.16499	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90714	0.841
1-1-2/M82	1.32074	1
12-2/M82	1.78732	1
12-4/M82	1.45647	1
1-3/M82	2.77636	0.248
2-1-1/M82	0.70424	0.565
2-1/M82	0.74366	0.325
2-6/M82	0.87241	1
3-2/M82	1.57336	0.84
4-1-1/M82	0.88022	1
4-1/M82	1.97131
4-3-2/M82	1.46682	0.246
4-3/M82	0.98883	1
5-3/M82	0.97659	1
6-2/M82	0.99941
6-3/M82	1.17905	1
7-1/M82	1.12086	0.992
7-2/M82	1.00226	1
9-3-2/M82	1.54543	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15314	0.277
IL2-6/WTpooled	1.18914	0.419
IL7-5/WTpooled	1.36452	0.792
IL7-3/WTpooled	1.02384	1
IL12-4/WTpooled	1.01843	0.891
IL1-4/WTpooled	1.25601	0.426
WT/WTpooled	1.00389	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	1.65921	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04924	0.921
DC3000/delta hrp 6h	1.16383	1
DC3000/delta hrp 12h	1.73122	1
DC3000/delta hrp 24h	0.73543	0.313

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71339	0.03
DC3000 delta B/DC3000 delta AB	1.08054	0.51

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00733	1
Exp 36h	1.77274	1
Exp 60h	1.61951	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96856	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.13796	0.692
Var 12h NI row2-row1	1.65584	0.266
Var 36h I row2-row1	1.22987	0.309
Var 36h NI row2-row1	0.74939	0.45
Var 60h I row2-row1	0.54082	0.285
Var 60h NI row2-row1	0.83171	0.818
Time course 0hI-0hNI	1.26572	0.537
Time course 12hI-12hNI	1.09651	0.741
Time course 36hI-36hNI	1.32949	0.014
Time course 60hI-60hNI	4.00741	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)	0.76791	0.286
transgenic ySAMdc/azygous control (breaker)	1.0988	0.248
transgenic ySAMdc/azygous control (red)	0.90966	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.539	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.59894	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05658	0.307
Manapal/WT (break)	0.98336	1
Manapal/WT (red)	0.80198	0.181