Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6754	0.029
27DAP/17DAP	0.76187	0.268
39DAP/27DAP	1.86349	0.038
41DAP/39DAP	0.62167	0.068
42DAP/41DAP	0.99265	1
43DAP/42DAP	1.06304	1
47DAP/43DAP	0.41718	0.049
52DAP/47DAP	1.31712	0.53
57DAP/52DAP	1.21592	0.886

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8561	0.007
17DAP/reference	1.0407	0.858
27DAP/reference	0.69122	0.015
39DAP/reference	0.70847	0.029
41DAP/reference	0.8028	0.039
42DAP/reference	1.02301	1
43DAP/reference	0.82155	0.056
47DAP/reference	0.78698	0.001
52DAP/reference	0.51053	0.013
57DAP/reference	0.66865	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82328	0.05
27DAP/17DAP	1.04539	0.905
39DAP/27DAP	0.8523	0.188
41DAP/39DAP	1.20622	1
42DAP/41DAP	1.05803	0.947
43DAP/42DAP	0.89169	0.132
47DAP/43DAP	0.95322	0.701
52DAP/47DAP	0.59438	0.042
57DAP/52DAP	0.88053	0.498
57DAP/7DAP	0.25697	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.28684	0.024
17DAP/reference	2.134	0.006
27DAP/reference	1.48086	0.018
39DAP/reference	1.25703	0.133
41DAP/reference	1.59084	0.015
42DAP/reference	1.5463	0.012
43DAP/reference	1.29863	0.037
47DAP/reference	1.36986	0.018
52DAP/reference	1.27616	0.171
57DAP/reference	0.96798	0.411

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34116	0.083
17DAP/reference	1.70887	0.01
27DAP/reference	1.33551	0.048
39DAP/reference	0.9268	0.144
41DAP/reference	1.16514	0.149
42DAP/reference	1.35163	0.031
43DAP/reference	0.77954	0.042
47DAP/reference	1.06179	0.498
52DAP/reference	0.69953	0.021
57DAP/reference	0.70625	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.30095	0.016
17DAP/reference	1.5269	0.206
27DAP/reference	1.54209	0.024
39DAP/reference	1.42867	0.016
41DAP/reference	1.04138	0.605
42DAP/reference	1.05088	0.658
43DAP/reference	0.95569	0.484
47DAP/reference	0.5564	0.01
52DAP/reference	0.90032	0.284
57DAP/reference	0.73781	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08976	0.966
26DAP/20DAP	3.22207	0.12
34DAP/26DAP	0.64388	0.147
51DAP/34DAP	0.90649	0.563
52DAP/51DAP	0.93556	1
53DAP/52DAP	0.79607	0.198
55DAP/53DAP	0.83601	0.195
57DAP/55DAP	1.00825	0.909
62DAP/57DAP	1.00827	1
68DAP/62DAP	1.06639	0.984
68DAP/14DAP	1.42213	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.25317	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04161	0.417
Mature Green Tomato/Ripe Tomato	2.28078	0.04
Immature Eggplant/Mature Eggplant	0.95688	0.594
Ripe Pepper/Ripe Tomato	1.2068	1
Mature Eggplant/Ripe Tomato	2.09217	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.933	0.944
1-1-2/M82	1.26499	1
12-2/M82	0.72081	0.727
12-4/M82	1.02831	1
1-3/M82	1.58033	0.277
2-1-1/M82	1.06199	1
2-1/M82	0.97758	1
2-6/M82	1.30951	0.505
3-2/M82	1.03964
4-1-1/M82	1.55395	1
4-1/M82	1.52578	1
4-3-2/M82	2.09233	0.241
4-3/M82	1.33385	1
5-3/M82	1.34602	0.572
6-2/M82	2.34985	0.211
6-3/M82	1.02041	1
7-1/M82	N/A	N/A
7-2/M82	1.69527	0.385
9-3-2/M82	1.73693	0.171

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.33168	0.277
IL2-6/WTpooled	1.0793	0.788
IL7-5/WTpooled	0.69034	1
IL7-3/WTpooled	0.9458	1
IL12-4/WTpooled	1.10117	0.516
IL1-4/WTpooled	0.8821	0.457
WT/WTpooled	0.95355	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	1.18275	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03358	0.921
DC3000/delta hrp 6h	1.02873	1
DC3000/delta hrp 12h	1.16121	1
DC3000/delta hrp 24h	1.29697	0.308

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.21758	0.055
DC3000 delta B/DC3000 delta AB	1.38202	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14632	1
Exp 36h	1.19093	0.693
Exp 60h	1.54707	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99306	1
Var 0h	0.99204	1
Var 12h I row2-row1	0.97844	0.948
Var 12h NI row2-row1	1.10401	0.281
Var 36h I row2-row1	1.1651	0.908
Var 36h NI row2-row1	0.93714	0.61
Var 60h I row2-row1	0.911	0.285
Var 60h NI row2-row1	0.80485	0.866
Time course 0hI-0hNI	1.08053	0.63
Time course 12hI-12hNI	1.05386	0.747
Time course 36hI-36hNI	1.44244	0.005
Time course 60hI-60hNI	1.51834	0.012

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)	1.1371	0.372
transgenic ySAMdc/azygous control (breaker)	1.13017	1
transgenic ySAMdc/azygous control (red)	1.21032	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22498	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72568	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.6022	0.307
Manapal/WT (break)	0.94917	1
Manapal/WT (red)	0.91996	0.607