Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89887	0.689
27DAP/17DAP	0.98587	1
39DAP/27DAP	0.75272	0.573
41DAP/39DAP	1.13282	0.788
42DAP/41DAP	0.88634	1
43DAP/42DAP	1.11428	1
47DAP/43DAP	1.45239	0.233
52DAP/47DAP	1.16223	0.964
57DAP/52DAP	1.26239	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74212	0.063
17DAP/reference	0.81739	0.368
27DAP/reference	1.23943	0.15
39DAP/reference	1.20443
41DAP/reference	0.98016	0.814
42DAP/reference	0.92811	0.169
43DAP/reference	0.60963
47DAP/reference	0.85893	0.207
52DAP/reference	0.96348	0.564
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14632	0.699
27DAP/17DAP	1.14186	0.694
39DAP/27DAP	1.46325	0.096
41DAP/39DAP	1.45866	0.197
42DAP/41DAP	0.94943	0.687
43DAP/42DAP	0.86618	0.293
47DAP/43DAP	1.73284	0.008
52DAP/47DAP	0.69768	0.119
57DAP/52DAP	1.51862	0.177
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08376	1
17DAP/reference	0.74475	0.018
27DAP/reference	0.95516	0.283
39DAP/reference	0.65255	0.011
41DAP/reference	0.69931	0.016
42DAP/reference	0.69787	0.01
43DAP/reference	0.8124	0.11
47DAP/reference	0.88416	0.222
52DAP/reference	0.74386	0.012
57DAP/reference	0.96774	0.426

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88073	0.306
17DAP/reference	0.77096	0.039
27DAP/reference	0.91449	0.438
39DAP/reference	0.71919	0.071
41DAP/reference	0.7626	0.13
42DAP/reference	0.85947	0.055
43DAP/reference	1.06945	0.957
47DAP/reference	0.89245	0.061
52DAP/reference	0.91927	0.22
57DAP/reference	0.94528	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92842	0.092
17DAP/reference	0.85024	0.064
27DAP/reference	0.82134	0.06
39DAP/reference	0.80667	0.01
41DAP/reference	0.83182	0.086
42DAP/reference	0.82595	0.059
43DAP/reference	0.99699	0.858
47DAP/reference	0.94952	0.371
52DAP/reference	0.86037	0.2
57DAP/reference	1.07312	0.57

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12233	1
26DAP/20DAP	1.11433	0.941
34DAP/26DAP	1.27334	1
51DAP/34DAP	1.76019	0.032
52DAP/51DAP	0.93275	1
53DAP/52DAP	1.38639	0.517
55DAP/53DAP	0.90387	0.698
57DAP/55DAP	1.01271	0.96
62DAP/57DAP	0.92834	0.871
68DAP/62DAP	1.91056	0.022
68DAP/14DAP	1.43661	0.119

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.77144	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.14286	0.008
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.58446	0.293
Mature Eggplant/Ripe Tomato	0.35639	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.19982	1
12-2/M82	1.55866
12-4/M82	0.89032
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	1.0334	1
6-2/M82	N/A	N/A
6-3/M82	0.79341
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.25739	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.02989	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.05155	1
WT/WTpooled	N/A	N/A

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	1.07758	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91492
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.71587	0.24
DC3000/delta hrp 24h	9.19876	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.36029
DC3000 delta B/DC3000 delta AB	0.90937	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.96289	0.943
Exp 60h	1.20483	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0355	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.02708	0.654
Var 12h NI row2-row1	1.15455	0.649
Var 36h I row2-row1	0.86967	0.575
Var 36h NI row2-row1	2.25388	1
Var 60h I row2-row1	0.91076	0.285
Var 60h NI row2-row1	0.87109	0.292
Time course 0hI-0hNI	1.03679	0.852
Time course 12hI-12hNI	1.14828	0.461
Time course 36hI-36hNI	1.66666	0.005
Time course 60hI-60hNI	2.97629	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)	2.19814	0.455
transgenic ySAMdc/azygous control (breaker)	0.72133	0.139
transgenic ySAMdc/azygous control (red)	1.00353	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0381	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12254	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02056	1
Manapal/WT (break)	0.54468	0.299
Manapal/WT (red)	0.30211	0.181