Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.4.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07621	0.912
27DAP/17DAP	1.24016	0.799
39DAP/27DAP	0.83032	0.364
41DAP/39DAP	1.29824	0.504
42DAP/41DAP	0.91869	1
43DAP/42DAP	0.98354	0.93
47DAP/43DAP	1.15706	0.442
52DAP/47DAP	0.82069	0.512
57DAP/52DAP	0.93036	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00029	0.787
17DAP/reference	1.04787	0.031
27DAP/reference	0.98029	0.514
39DAP/reference	1.01712	0.722
41DAP/reference	0.98143	0.667
42DAP/reference	0.98197	0.169
43DAP/reference	1.05592	0.425
47DAP/reference	1.0296	0.558
52DAP/reference	0.89937	0.223
57DAP/reference	0.99804	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94065	0.428
27DAP/17DAP	1.01704	0.967
39DAP/27DAP	1.0747	0.483
41DAP/39DAP	0.9725	0.968
42DAP/41DAP	1.14303	0.571
43DAP/42DAP	0.94522	0.293
47DAP/43DAP	0.96188	0.833
52DAP/47DAP	1.32267	0.422
57DAP/52DAP	1.43272	0.069
57DAP/7DAP	1.49804	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14819	0.83
17DAP/reference	1.49144	0.199
27DAP/reference	1.3573	0.008
39DAP/reference	1.227	0.222
41DAP/reference	1.08798	0.093
42DAP/reference	1.1697	0.889
43DAP/reference	1.46905	0.006
47DAP/reference	0.93062	0.222
52DAP/reference	N/A	N/A
57DAP/reference	1.82317	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94084	0.353
17DAP/reference	1.01026	1
27DAP/reference	1.22307	0.822
39DAP/reference	0.8967	0.147
41DAP/reference	0.94911	0.315
42DAP/reference	0.93798	0.169
43DAP/reference	0.95336	0.43
47DAP/reference	0.95025	0.214
52DAP/reference	1.01443	0.789
57DAP/reference	1.03072	0.737

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10727	0.078
17DAP/reference	1.07668	0.977
27DAP/reference	1.91062	0.039
39DAP/reference	1.96919	0.041
41DAP/reference	1.60722	0.156
42DAP/reference	1.33924	0.356
43DAP/reference	1.19651	0.209
47DAP/reference	0.93013	0.161
52DAP/reference	1.62587	0.499
57DAP/reference	1.0031	0.613

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02704	0.966
26DAP/20DAP	1.94615	0.22
34DAP/26DAP	1.53025	1
51DAP/34DAP	1.32202	0.854
52DAP/51DAP	2.23153	0.033
53DAP/52DAP	0.61917
55DAP/53DAP	1.50186	0.599
57DAP/55DAP	0.74731	0.168
62DAP/57DAP	1.01627	1
68DAP/62DAP	1.13145	0.878
68DAP/14DAP	0.9892	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.44443	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.52169	0.058
Mature Green Tomato/Ripe Tomato	1.00499	0.715
Immature Eggplant/Mature Eggplant	1.94908	0.05
Ripe Pepper/Ripe Tomato	1.06665	1
Mature Eggplant/Ripe Tomato	2.62885	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05071	0.877
1-1-2/M82	1.01048	1
12-2/M82	1.02084	1
12-4/M82	0.96834	1
1-3/M82	0.98522
2-1-1/M82	1.05435	0.689
2-1/M82	1.50964	0.345
2-6/M82	0.93422	1
3-2/M82	0.99903	1
4-1-1/M82	1.09178	1
4-1/M82	0.96293	0.737
4-3-2/M82	1.00458	1
4-3/M82	1.03635	1
5-3/M82	1.04206	1
6-2/M82	1.09415	1
6-3/M82	1.01445	1
7-1/M82	0.97791	1
7-2/M82	1.02026	1
9-3-2/M82	0.9547	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88138	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	4.70968	1
IL12-4/WTpooled	1.71005	0.516
IL1-4/WTpooled	2.48704
WT/WTpooled	1.01413	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	0.83211	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97039	1
DC3000/delta hrp 6h	1.05588	1
DC3000/delta hrp 12h	0.99782	1
DC3000/delta hrp 24h	1.04456	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.75934	0.145
DC3000 delta B/DC3000 delta AB	1.22839	0.199

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93242	1
Exp 36h	1.14558	1
Exp 60h	1.0168	1

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.03691	0.541
transgenic ySAMdc/azygous control (breaker)	0.82477	0.15
transgenic ySAMdc/azygous control (red)	0.98921	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99448	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7637	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83931	1
Manapal/WT (break)	1.10667	1
Manapal/WT (red)	1.16248	0.413