Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90042	0.486
27DAP/17DAP	0.90681	0.804
39DAP/27DAP	1.10953	0.857
41DAP/39DAP	1.37802	0.553
42DAP/41DAP	1.18545	0.856
43DAP/42DAP	0.74666	0.55
47DAP/43DAP	0.66641	0.185
52DAP/47DAP	2.21743	0.191
57DAP/52DAP	0.6548	0.622

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08404	0.441
17DAP/reference	0.93969	0.321
27DAP/reference	1.08034	0.539
39DAP/reference	1.39031	0.032
41DAP/reference	1.11919	0.203
42DAP/reference	1.1221	0.174
43DAP/reference	0.97761	0.631
47DAP/reference	1.02306	0.636
52DAP/reference	1.10794	0.498
57DAP/reference	1.29275	0.18

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85247	0.311
27DAP/17DAP	0.92168	0.748
39DAP/27DAP	1.19877	0.471
41DAP/39DAP	1.17237	0.497
42DAP/41DAP	0.92236	0.503
43DAP/42DAP	1.08487	0.297
47DAP/43DAP	0.95127	0.805
52DAP/47DAP	1.02275	1
57DAP/52DAP	0.85601	0.32
57DAP/7DAP	0.66931	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8574	0.326
17DAP/reference	0.9182	0.22
27DAP/reference	1.45197	0.011
39DAP/reference	0.87859	0.146
41DAP/reference	1.10232	0.232
42DAP/reference	1.24016	0.014
43DAP/reference	0.92774	0.175
47DAP/reference	1.01831	0.98
52DAP/reference	1.04788	0.563
57DAP/reference	0.80703	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46636	0.038
17DAP/reference	1.61936	0.012
27DAP/reference	1.82789	0.014
39DAP/reference	1.4734	0.014
41DAP/reference	1.41423	0.072
42DAP/reference	1.7772	0.007
43DAP/reference	2.55819	0.011
47DAP/reference	1.81221	0.011
52DAP/reference	1.54874	0.008
57DAP/reference	1.33233	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92531	0.391
17DAP/reference	1.09778	0.824
27DAP/reference	0.86739	0.218
39DAP/reference	0.96839	0.504
41DAP/reference	1.30215	0.537
42DAP/reference	1.55665	0.013
43DAP/reference	1.39217	0.499
47DAP/reference	1.29843	0.011
52DAP/reference	1.27044	0.063
57DAP/reference	2.16609	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21954	0.966
26DAP/20DAP	0.99358	1
34DAP/26DAP	1.25491	0.819
51DAP/34DAP	0.83629	0.102
52DAP/51DAP	0.94337	1
53DAP/52DAP	0.96091	0.862
55DAP/53DAP	1.28354	0.341
57DAP/55DAP	1.14779	1
62DAP/57DAP	1.20482	0.678
68DAP/62DAP	1.107	0.84
68DAP/14DAP	1.02297	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.01129	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1132	0.666
Mature Green Tomato/Ripe Tomato	0.98953	0.774
Immature Eggplant/Mature Eggplant	0.79422	0.1
Ripe Pepper/Ripe Tomato	0.59401	0.224
Mature Eggplant/Ripe Tomato	0.64224	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09324	0.742
1-1-2/M82	1.02665	1
12-2/M82	N/A	N/A
12-4/M82	0.89308	1
1-3/M82	1.27043
2-1-1/M82	1.03416
2-1/M82	N/A	N/A
2-6/M82	0.91205	0.501
3-2/M82	0.78509
4-1-1/M82	0.8682	0.792
4-1/M82	0.8167	1
4-3-2/M82	0.93645	1
4-3/M82	1.04357	1
5-3/M82	1.07546	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.98723
7-2/M82	0.90894	0.578
9-3-2/M82	0.87493	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	1.41219
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	1.32831	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10624	0.914
DC3000/delta hrp 6h	0.99253	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.99013	1

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	0.32263

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01847	1
Exp 36h	0.903	0.879
Exp 60h	1.02599	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9632	1
Var 0h	1.00285	1
Var 12h I row2-row1	1.09037	0.406
Var 12h NI row2-row1	0.81804	0.494
Var 36h I row2-row1	0.84194	1
Var 36h NI row2-row1	0.92501	0.522
Var 60h I row2-row1	1.08887	0.562
Var 60h NI row2-row1	0.95573	1
Time course 0hI-0hNI	0.9357	0.347
Time course 12hI-12hNI	1.03436	0.684
Time course 36hI-36hNI	1.21008	0.089
Time course 60hI-60hNI	1.3473	0.029

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)	0.88298	0.267
transgenic ySAMdc/azygous control (breaker)	1.82061	0.248
transgenic ySAMdc/azygous control (red)	1.21057	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07758	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69145	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88874	1
Manapal/WT (break)	1.14102	1
Manapal/WT (red)	1.13477	0.413