Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8757	0.445
27DAP/17DAP	0.98703	1
39DAP/27DAP	1.45498	0.121
41DAP/39DAP	0.79209	0.283
42DAP/41DAP	1.15921	0.898
43DAP/42DAP	1.0927	1
47DAP/43DAP	0.94996	0.76
52DAP/47DAP	0.96682	0.8
57DAP/52DAP	1.0393	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02514	0.96
17DAP/reference	0.98978	0.819
27DAP/reference	0.97035	0.61
39DAP/reference	1.37289	0.021
41DAP/reference	1.11463	0.122
42DAP/reference	1.12817	0.352
43DAP/reference	1.13239	0.026
47DAP/reference	1.02401	0.764
52DAP/reference	1.02097	1
57DAP/reference	1.0736	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9811	0.732
27DAP/17DAP	1.12373	0.694
39DAP/27DAP	0.94899	0.673
41DAP/39DAP	1.10726	0.674
42DAP/41DAP	0.93015	0.443
43DAP/42DAP	1.01136	0.699
47DAP/43DAP	0.90666	0.28
52DAP/47DAP	0.92536	0.666
57DAP/52DAP	0.98475	0.784
57DAP/7DAP	1.14217	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9269	0.326
17DAP/reference	1.0194	1
27DAP/reference	1.35336	0.018
39DAP/reference	0.8619	0.056
41DAP/reference	1.05037	0.507
42DAP/reference	1.13192	0.03
43DAP/reference	1.32148	0.029
47DAP/reference	1.36538	0.059
52DAP/reference	1.28942	0.038
57DAP/reference	1.1385	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10255	0.495
17DAP/reference	1.44675	0.022
27DAP/reference	1.47554	0.03
39DAP/reference	1.32683	0.018
41DAP/reference	1.47638	0.005
42DAP/reference	1.42977	0.009
43DAP/reference	1.91465	0.112
47DAP/reference	1.49942	0.009
52DAP/reference	1.26514	0.069
57DAP/reference	1.17282	0.07

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05195	0.709
17DAP/reference	1.10201	0.558
27DAP/reference	1.17563	0.125
39DAP/reference	1.16594	0.027
41DAP/reference	1.20008	0.181
42DAP/reference	1.26463	0.02
43DAP/reference	0.95194	0.484
47DAP/reference	1.23797	0.006
52DAP/reference	1.12634	0.42
57DAP/reference	1.52741	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8192	0.733
26DAP/20DAP	1.14445	0.587
34DAP/26DAP	0.8405	0.735
51DAP/34DAP	0.7953	0.109
52DAP/51DAP	0.9005	1
53DAP/52DAP	1.11032	1
55DAP/53DAP	1.0851	0.671
57DAP/55DAP	1.23804	1
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.61783	0.034
68DAP/14DAP	1.99289	0.069

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.47574	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.89804	0.471
Mature Green Tomato/Ripe Tomato	0.98498	0.835
Immature Eggplant/Mature Eggplant	0.70758	0.068
Ripe Pepper/Ripe Tomato	1.38163	1
Mature Eggplant/Ripe Tomato	1.3556	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91268	0.616
1-1-2/M82	1.19885	1
12-2/M82	0.99711	1
12-4/M82	0.81883	0.358
1-3/M82	2.50812
2-1-1/M82	1.02185	0.764
2-1/M82	0.75347	0.322
2-6/M82	0.91074	1
3-2/M82	0.86859	0.455
4-1-1/M82	N/A	N/A
4-1/M82	1.19017
4-3-2/M82	1.61308
4-3/M82	1.52541	0.268
5-3/M82	0.96414	1
6-2/M82	1.16057
6-3/M82	1.01547	1
7-1/M82	1.02429	1
7-2/M82	0.97178	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.62217	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97682	1
IL12-4/WTpooled	0.94252	0.71
IL1-4/WTpooled	1.02015
WT/WTpooled	1.09326	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	0.96983	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03778	0.914
DC3000/delta hrp 6h	1.10491	0.978
DC3000/delta hrp 12h	1.00545	1
DC3000/delta hrp 24h	0.9494	0.654

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04985
DC3000 delta B/DC3000 delta AB	1.24252	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17044	1
Exp 36h	1.02748	1
Exp 60h	1.24205	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02209	1
Var 0h	1.33392	0.289
Var 12h I row2-row1	0.92325	0.565
Var 12h NI row2-row1	1.2176	0.649
Var 36h I row2-row1	1.20471	0.309
Var 36h NI row2-row1	0.81754	0.469
Var 60h I row2-row1	0.85734	0.582
Var 60h NI row2-row1	0.84631	0.63
Time course 0hI-0hNI	0.98798	0.935
Time course 12hI-12hNI	0.99673	1
Time course 36hI-36hNI	1.22074	0.05
Time course 60hI-60hNI	1.87808	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)	0.87793	0.3
transgenic ySAMdc/azygous control (breaker)	1.15344	0.248
transgenic ySAMdc/azygous control (red)	0.9638	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14152	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.706	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93434	1
Manapal/WT (break)	0.80377	0.333
Manapal/WT (red)	0.98794	0.863