Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02323	0.901
27DAP/17DAP	0.66787	0.158
39DAP/27DAP	1.05525	0.915
41DAP/39DAP	0.73185	0.147
42DAP/41DAP	0.6733	0.397
43DAP/42DAP	0.81691	0.705
47DAP/43DAP	0.71274	0.18
52DAP/47DAP	1.26026	0.608
57DAP/52DAP	0.97693	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96442	0.379
17DAP/reference	1.0124	0.787
27DAP/reference	1.06771	0.559
39DAP/reference	1.12485	0.076
41DAP/reference	0.91985	0.341
42DAP/reference	1.08702	0.151
43DAP/reference	1.04921	0.705
47DAP/reference	1.06794	0.295
52DAP/reference	1.00957	1
57DAP/reference	1.09265	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.78078	0.053
27DAP/17DAP	0.9489	0.854
39DAP/27DAP	0.43773	0.029
41DAP/39DAP	1.28607	0.827
42DAP/41DAP	0.92631	0.515
43DAP/42DAP	0.73342	0.04
47DAP/43DAP	0.93143	0.554
52DAP/47DAP	1.01168	0.979
57DAP/52DAP	1.12069	0.489
57DAP/7DAP	0.55229	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.02992	0.033
17DAP/reference	1.88806	0.008
27DAP/reference	1.33804	0.018
39DAP/reference	1.04859	0.46
41DAP/reference	1.3605	0.025
42DAP/reference	1.28082	0.046
43DAP/reference	1.32201	0.105
47DAP/reference	1.13123	0.224
52DAP/reference	2.01293	0.008
57DAP/reference	1.50084	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16206	0.156
17DAP/reference	1.12534	0.043
27DAP/reference	1.1015	0.235
39DAP/reference	1.01068	0.745
41DAP/reference	0.96454	0.307
42DAP/reference	1.01846	1
43DAP/reference	1.21113	0.179
47DAP/reference	0.89917	0.302
52DAP/reference	1.11096	0.393
57DAP/reference	1.36047	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.62461	0.015
17DAP/reference	1.34674	0.046
27DAP/reference	1.19515	0.081
39DAP/reference	1.05992	0.342
41DAP/reference	0.95325	0.459
42DAP/reference	0.74667	0.071
43DAP/reference	0.87258	0.237
47DAP/reference	1.26142	0.016
52DAP/reference	0.74263	0.164
57DAP/reference	1.05645	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.38311	0.966
26DAP/20DAP	2.18861	0.099
34DAP/26DAP	0.66905	0.139
51DAP/34DAP	1.10825	0.597
52DAP/51DAP	1.1112	0.387
53DAP/52DAP	0.96893	0.79
55DAP/53DAP	0.91472	0.336
57DAP/55DAP	1.08831	0.841
62DAP/57DAP	0.99241	1
68DAP/62DAP	1.05078	0.899
68DAP/14DAP	1.12803	0.504

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22504	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11926
Mature Green Tomato/Ripe Tomato	3.6519	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	4.77233	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78003	0.512
1-1-2/M82	0.89235	1
12-2/M82	1.07356	1
12-4/M82	0.8809	1
1-3/M82	0.98914	1
2-1-1/M82	0.92549	0.784
2-1/M82	0.77567
2-6/M82	1.11888	0.505
3-2/M82	0.94879
4-1-1/M82	1.05634	1
4-1/M82	1.0851	0.466
4-3-2/M82	0.88412	0.698
4-3/M82	0.68813
5-3/M82	1.01192	1
6-2/M82	0.98768	0.473
6-3/M82	0.95079	1
7-1/M82	N/A	N/A
7-2/M82	0.9099	0.881
9-3-2/M82	0.74854	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.22615	0.493
IL2-6/WTpooled	1.15797	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98268	1
IL12-4/WTpooled	0.82348	0.71
IL1-4/WTpooled	1.1341
WT/WTpooled	0.94367	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	0.91609	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98571	1
DC3000/delta hrp 6h	1.10514	1
DC3000/delta hrp 12h	1.04724	1
DC3000/delta hrp 24h	0.95964	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76314	0.028
DC3000 delta B/DC3000 delta AB	0.83297	0.085

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87428	1
Exp 36h	0.92853	0.879
Exp 60h	0.93649	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9954	1
Var 0h	0.75373	0.457
Var 12h I row2-row1	1.08533	0.692
Var 12h NI row2-row1	0.9866	1
Var 36h I row2-row1	0.87458	1
Var 36h NI row2-row1	1.52425	1
Var 60h I row2-row1	0.91102	0.374
Var 60h NI row2-row1	1.13023	0.904
Time course 0hI-0hNI	0.9497	0.721
Time course 12hI-12hNI	1.02943	0.811
Time course 36hI-36hNI	0.86655	0.132
Time course 60hI-60hNI	0.74244	0.011

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)	0.98283	0.789
transgenic ySAMdc/azygous control (breaker)	1.55372	0.166
transgenic ySAMdc/azygous control (red)	1.00373	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00949	0.587

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2317	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.81539	0.093
Manapal/WT (break)	1.33324	0.14
Manapal/WT (red)	1.58492	0.413