Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49923	0.561
27DAP/17DAP	1.24226	0.808
39DAP/27DAP	1.02367	0.84
41DAP/39DAP	0.91811	0.646
42DAP/41DAP	1.16435	0.752
43DAP/42DAP	1.12229	0.892
47DAP/43DAP	1.24209	0.576
52DAP/47DAP	0.82138	0.545
57DAP/52DAP	1.32575	0.764

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11649	0.403
17DAP/reference	0.88899	0.147
27DAP/reference	0.98019	0.668
39DAP/reference	0.85716	0.058
41DAP/reference	0.84873	0.026
42DAP/reference	1.14948	0.287
43DAP/reference	1.0098	1
47DAP/reference	1.24093	0.011
52DAP/reference	1.39957	0.027
57DAP/reference	1.17945	0.105

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17095	0.414
27DAP/17DAP	0.90835	0.648
39DAP/27DAP	1.1145	0.483
41DAP/39DAP	1.0048	1
42DAP/41DAP	1.16019	0.401
43DAP/42DAP	1.07736	0.446
47DAP/43DAP	0.9816	0.902
52DAP/47DAP	0.89512	0.42
57DAP/52DAP	0.83044	0.337
57DAP/7DAP	0.94964	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98616	0.613
17DAP/reference	1.20257	0.092
27DAP/reference	1.23744	0.107
39DAP/reference	1.08764	0.133
41DAP/reference	1.04161	0.655
42DAP/reference	1.15376	0.174
43DAP/reference	1.20679	0.14
47DAP/reference	1.32323	0.068
52DAP/reference	1.46573	0.017
57DAP/reference	1.34841	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06927	0.597
17DAP/reference	1.29079	0.019
27DAP/reference	1.29091	0.07
39DAP/reference	1.46695	0.106
41DAP/reference	1.48004	0.012
42DAP/reference	1.26835	0.03
43DAP/reference	1.03811	0.892
47DAP/reference	1.21439	0.043
52DAP/reference	1.1354	0.747
57DAP/reference	1.08041	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11959	0.356
17DAP/reference	1.01687	0.944
27DAP/reference	0.8823	0.056
39DAP/reference	1.02919	0.691
41DAP/reference	1.08972	0.231
42DAP/reference	1.16568	0.416
43DAP/reference	1.46951	0.021
47DAP/reference	1.17175	0.085
52DAP/reference	1.21901	0.186
57DAP/reference	1.53443	0.05

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07897	1
26DAP/20DAP	0.9979	1
34DAP/26DAP	1.11452	0.819
51DAP/34DAP	0.83468	0.41
52DAP/51DAP	1.15461	0.51
53DAP/52DAP	1.06391	0.858
55DAP/53DAP	1.15264	0.861
57DAP/55DAP	0.98679	0.909
62DAP/57DAP	0.78114	0.681
68DAP/62DAP	1.13277	0.885
68DAP/14DAP	1.90888	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26554	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70242	0.188
Mature Green Tomato/Ripe Tomato	0.64167	0.017
Immature Eggplant/Mature Eggplant	1.02952	0.507
Ripe Pepper/Ripe Tomato	1.02478	1
Mature Eggplant/Ripe Tomato	0.82507	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85768
1-1-2/M82	1.58803
12-2/M82	0.80436
12-4/M82	0.99328	1
1-3/M82	2.22438
2-1-1/M82	1.13335	0.422
2-1/M82	N/A	N/A
2-6/M82	0.99238	1
3-2/M82	1.07407
4-1-1/M82	0.97715	1
4-1/M82	1.14435	1
4-3-2/M82	1.33117	0.508
4-3/M82	1.4608	0.268
5-3/M82	1.12269	1
6-2/M82	1.12951	1
6-3/M82	0.89163
7-1/M82	1.0649
7-2/M82	N/A	N/A
9-3-2/M82	1.45492	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.79246
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	1.18206	0.177

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10542	0.921
DC3000/delta hrp 6h	0.90332	0.95
DC3000/delta hrp 12h	0.95276	1
DC3000/delta hrp 24h	0.80312	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15148	0.333
DC3000 delta B/DC3000 delta AB	0.98143	1

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94928	1
Var 0h	0.9869	1
Var 12h I row2-row1	0.96014	0.856
Var 12h NI row2-row1	0.95038	0.906
Var 36h I row2-row1	1.09924	0.368
Var 36h NI row2-row1	0.98029	0.852
Var 60h I row2-row1	0.97623	1
Var 60h NI row2-row1	0.78781	0.516
Time course 0hI-0hNI	0.91384	0.225
Time course 12hI-12hNI	0.97502	0.795
Time course 36hI-36hNI	1.11805	0.063
Time course 60hI-60hNI	1.55454	0.042

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)	0.83845	0.229
transgenic ySAMdc/azygous control (breaker)	1.1392	0.248
transgenic ySAMdc/azygous control (red)	0.98984	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.20472	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63849	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20343	0.307
Manapal/WT (break)	0.98702	1
Manapal/WT (red)	1.14576	0.413