Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83257	0.166
27DAP/17DAP	1.1237	0.859
39DAP/27DAP	1.44552	0.13
41DAP/39DAP	0.831	0.288
42DAP/41DAP	1.17199	0.813
43DAP/42DAP	0.97988	0.925
47DAP/43DAP	1.02998	0.809
52DAP/47DAP	1.01531	0.999
57DAP/52DAP	1.30997	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30681	0.075
17DAP/reference	1.07018	0.717
27DAP/reference	1.02168	1
39DAP/reference	1.03515	1
41DAP/reference	0.93132	0.542
42DAP/reference	1.17758	0.035
43DAP/reference	1.13859	0.202
47DAP/reference	1.15878	0.003
52DAP/reference	1.14839	0.167
57DAP/reference	1.14951	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11068	0.334
27DAP/17DAP	0.9332	0.508
39DAP/27DAP	0.95908	0.587
41DAP/39DAP	0.9771	0.973
42DAP/41DAP	1.11515	0.316
43DAP/42DAP	0.96063	0.336
47DAP/43DAP	1.05019	0.844
52DAP/47DAP	1.16407	0.527
57DAP/52DAP	1.36251	0.153
57DAP/7DAP	0.80899	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39831	0.028
17DAP/reference	1.18917	0.077
27DAP/reference	1.28046	0.01
39DAP/reference	1.52293	0.005
41DAP/reference	1.18937	0.159
42DAP/reference	1.3114	0.018
43DAP/reference	1.4866	0.01
47DAP/reference	1.67136	0.014
52DAP/reference	1.6656	0.007
57DAP/reference	1.51287	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24004	0.495
17DAP/reference	1.0204	1
27DAP/reference	1.30445	0.128
39DAP/reference	1.19599	0.164
41DAP/reference	1.53121	0.031
42DAP/reference	1.25715	0.028
43DAP/reference	0.93982	0.43
47DAP/reference	1.14226	0.148
52DAP/reference	1.02884	1
57DAP/reference	0.96032	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39684	0.021
17DAP/reference	1.09004	0.42
27DAP/reference	1.13814	0.284
39DAP/reference	1.24942	0.022
41DAP/reference	1.32678	0.15
42DAP/reference	1.43936	0.007
43DAP/reference	1.5577	0.013
47DAP/reference	1.13601	0.877
52DAP/reference	1.15862	0.126
57DAP/reference	1.82389	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17228	0.966
26DAP/20DAP	1.53692	0.195
34DAP/26DAP	1.54236	0.819
51DAP/34DAP	0.88485	0.563
52DAP/51DAP	1.64739	0.047
53DAP/52DAP	0.96972	0.876
55DAP/53DAP	0.80514	0.325
57DAP/55DAP	0.60756	0.057
62DAP/57DAP	1.04334	1
68DAP/62DAP	2.07097	0.472
68DAP/14DAP	2.03253	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.67936	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.35211	0.058
Mature Green Tomato/Ripe Tomato	1.14476	0.752
Immature Eggplant/Mature Eggplant	1.25321	0.061
Ripe Pepper/Ripe Tomato	1.12972	0.258
Mature Eggplant/Ripe Tomato	1.41413	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20484	0.591
1-1-2/M82	1.08022	1
12-2/M82	1.0282	1
12-4/M82	1.0108	1
1-3/M82	1.25399	1
2-1-1/M82	0.95623	0.92
2-1/M82	0.83481	0.519
2-6/M82	0.94669	1
3-2/M82	0.83521
4-1-1/M82	0.99572	1
4-1/M82	1.32675	0.418
4-3-2/M82	1.0035	1
4-3/M82	1.1949	1
5-3/M82	0.96734	1
6-2/M82	1.04013	1
6-3/M82	0.99793	1
7-1/M82	0.93474	0.803
7-2/M82	1.02605	1
9-3-2/M82	1.12956	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95594
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03392	1
IL12-4/WTpooled	1.03183	1
IL1-4/WTpooled	0.96371	1
WT/WTpooled	1.18075	0.794

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	0.99338	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96949	1
DC3000/delta hrp 6h	0.87522	0.95
DC3000/delta hrp 12h	1.03888	1
DC3000/delta hrp 24h	0.91935	0.438

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89679	0.171
DC3000 delta B/DC3000 delta AB	0.93458	0.605

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24583	1
Exp 36h	N/A	N/A
Exp 60h	0.60725	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01789	1
Var 0h	0.9254	0.933
Var 12h I row2-row1	0.79216	0.418
Var 12h NI row2-row1	0.92948	0.627
Var 36h I row2-row1	0.89813	0.805
Var 36h NI row2-row1	2.61963	1
Var 60h I row2-row1	1.07273	0.543
Var 60h NI row2-row1	0.89361	0.977
Time course 0hI-0hNI	0.97928	0.935
Time course 12hI-12hNI	0.9142	0.219
Time course 36hI-36hNI	0.72868	0.023
Time course 60hI-60hNI	0.42308	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)	1.00009	0.931
transgenic ySAMdc/azygous control (breaker)	0.92124	0.49
transgenic ySAMdc/azygous control (red)	0.93195	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9661	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42625	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04003	1
Manapal/WT (break)	0.77687	0.333
Manapal/WT (red)	0.8516	0.242