Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06905	0.997
27DAP/17DAP	0.72655	0.196
39DAP/27DAP	0.78183	0.315
41DAP/39DAP	1.18952	0.473
42DAP/41DAP	0.68121	0.774
43DAP/42DAP	0.8872	0.713
47DAP/43DAP	0.95285	0.779
52DAP/47DAP	1.11984	0.997
57DAP/52DAP	0.93966	0.936

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09334	0.71
17DAP/reference	0.99581	0.904
27DAP/reference	1.06794	0.529
39DAP/reference	1.06345	0.486
41DAP/reference	1.00912	1
42DAP/reference	0.97029	0.259
43DAP/reference	1.01573	0.957
47DAP/reference	1.02948	1
52DAP/reference	0.95496	0.449
57DAP/reference	1.10824	0.109

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.55044	0.068
27DAP/17DAP	1.23299	0.156
39DAP/27DAP	0.59994	0.041
41DAP/39DAP	1.38218	0.024
42DAP/41DAP	0.68166	0.044
43DAP/42DAP	1.09649	0.478
47DAP/43DAP	0.9012	0.554
52DAP/47DAP	1.14328	0.603
57DAP/52DAP	0.96909	0.737
57DAP/7DAP	0.58746	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97945	0.495
17DAP/reference	1.17713	0.102
27DAP/reference	1.36814	0.008
39DAP/reference	1.13917	0.141
41DAP/reference	1.28315	0.117
42DAP/reference	1.31266	0.024
43DAP/reference	1.16771	0.325
47DAP/reference	1.20575	0.099
52DAP/reference	1.16724	0.459
57DAP/reference	0.88558	0.052

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2858	0.041
17DAP/reference	1.26417	0.018
27DAP/reference	1.12825	0.316
39DAP/reference	1.14969	0.225
41DAP/reference	1.04026	1
42DAP/reference	1.3561	0.015
43DAP/reference	1.29497	0.522
47DAP/reference	1.28713	0.008
52DAP/reference	1.21476	0.024
57DAP/reference	0.98883	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98123	0.566
17DAP/reference	1.25485	0.043
27DAP/reference	1.23864	0.048
39DAP/reference	1.0783	0.116
41DAP/reference	1.07539	0.174
42DAP/reference	1.28731	0.08
43DAP/reference	0.88366	0.171
47DAP/reference	1.04931	0.61
52DAP/reference	0.98863	0.781
57DAP/reference	0.8372	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98902	1
26DAP/20DAP	0.78992	0.244
34DAP/26DAP	0.9888	1
51DAP/34DAP	1.0045	0.863
52DAP/51DAP	1.2302	0.481
53DAP/52DAP	1.21971	0.697
55DAP/53DAP	0.85438	0.325
57DAP/55DAP	0.98523	0.859
62DAP/57DAP	0.94874	0.681
68DAP/62DAP	1.00675	1
68DAP/14DAP	0.86892	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61829	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.41915	0.399
Immature Eggplant/Mature Eggplant	0.29273
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20698	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.60352
1-3/M82	0.50101
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	0.86739
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	0.93615	1
6-2/M82	0.52799
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.94929
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.801	0.247
IL2-6/WTpooled	0.84616	0.383
IL7-5/WTpooled	1.04924	1
IL7-3/WTpooled	0.8176	0.31
IL12-4/WTpooled	1.08315	0.785
IL1-4/WTpooled	0.98839	1
WT/WTpooled	0.97528	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	1.27597	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06858	0.758
DC3000/delta hrp 6h	0.96161	0.95
DC3000/delta hrp 12h	1.07707	1
DC3000/delta hrp 24h	1.21002	0.151

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.38328	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06763	1
Exp 36h	0.97044	0.82
Exp 60h	0.82937	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06734	1
Var 0h	1.0575	0.263
Var 12h I row2-row1	1.60953	0.348
Var 12h NI row2-row1	0.83868	0.394
Var 36h I row2-row1	0.89441	0.438
Var 36h NI row2-row1	1.22138	1
Var 60h I row2-row1	1.05059	0.502
Var 60h NI row2-row1	1.09931	0.904
Time course 0hI-0hNI	1.12265	0.603
Time course 12hI-12hNI	0.88966	0.275
Time course 36hI-36hNI	0.65182	0.023
Time course 60hI-60hNI	0.59535	0.015

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)	0.88016	0.377
transgenic ySAMdc/azygous control (breaker)	0.86369	0.49
transgenic ySAMdc/azygous control (red)	0.96048	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97834	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92877	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.64852	0.14
Manapal/WT (break)	0.88661	1
Manapal/WT (red)	0.70767	0.187