Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.6.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91885	0.558
27DAP/17DAP	1.11327	0.845
39DAP/27DAP	0.88113	0.512
41DAP/39DAP	1.04675	0.894
42DAP/41DAP	0.96716	1
43DAP/42DAP	0.94264	0.874
47DAP/43DAP	1.32261	0.201
52DAP/47DAP	1.20176	0.541
57DAP/52DAP	1.16672	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84334	0.092
17DAP/reference	1.0822	0.148
27DAP/reference	1.02167	0.709
39DAP/reference	1.0402	0.557
41DAP/reference	1.08308	0.041
42DAP/reference	0.90305	0.035
43DAP/reference	1.11308	0.445
47DAP/reference	1.16387	0.012
52DAP/reference	0.97768	0.504
57DAP/reference	0.89309	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64517	0.036
27DAP/17DAP	1.15428	0.344
39DAP/27DAP	0.94161	0.594
41DAP/39DAP	1.08732	0.781
42DAP/41DAP	0.96604	0.708
43DAP/42DAP	1.07568	0.324
47DAP/43DAP	0.97684	0.896
52DAP/47DAP	0.97935	0.905
57DAP/52DAP	0.96525	0.705
57DAP/7DAP	0.93484	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04257	0.91
17DAP/reference	0.80252	0.108
27DAP/reference	0.86543	0.264
39DAP/reference	1.01897	1
41DAP/reference	0.95152	0.394
42DAP/reference	0.96046	0.436
43DAP/reference	1.19451	0.256
47DAP/reference	0.88187	0.293
52DAP/reference	1.17519	0.121
57DAP/reference	1.11069	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8863	0.157
17DAP/reference	0.92292	0.077
27DAP/reference	0.82475	0.123
39DAP/reference	0.85646	0.091
41DAP/reference	0.82601	0.056
42DAP/reference	0.89031	0.189
43DAP/reference	0.95544	0.468
47DAP/reference	0.9618	0.201
52DAP/reference	0.94545	0.239
57DAP/reference	0.89144	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09179	0.456
17DAP/reference	1.02235	0.934
27DAP/reference	0.95281	0.594
39DAP/reference	0.83949	0.222
41DAP/reference	1.33658	0.174
42DAP/reference	1.16378	0.671
43DAP/reference	1.09209	1
47DAP/reference	1.22733	0.007
52DAP/reference	1.34664	0.118
57DAP/reference	0.85608	0.177

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00556	1
26DAP/20DAP	1.11525	0.581
34DAP/26DAP	0.90153	0.404
51DAP/34DAP	0.89625	0.246
52DAP/51DAP	0.98303	1
53DAP/52DAP	0.99888	1
55DAP/53DAP	1.01074	1
57DAP/55DAP	1.01153	1
62DAP/57DAP	1.12329	0.622
68DAP/62DAP	0.8616	0.177
68DAP/14DAP	0.88405	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85693	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.66498	0.028
Immature Eggplant/Mature Eggplant	1.73479
Ripe Pepper/Ripe Tomato	1.25087	1
Mature Eggplant/Ripe Tomato	2.23719	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03709	1
1-1-2/M82	0.88666	0.958
12-2/M82	1.03085	1
12-4/M82	1.07235	1
1-3/M82	0.80326	0.33
2-1-1/M82	1.0842	1
2-1/M82	0.91991	0.322
2-6/M82	1.23455	0.594
3-2/M82	1.05628	0.549
4-1-1/M82	1.0256	1
4-1/M82	1.04591	1
4-3-2/M82	1.07206	1
4-3/M82	0.97645	1
5-3/M82	0.98986	1
6-2/M82	1.00708	1
6-3/M82	0.90595	0.857
7-1/M82	0.96028	1
7-2/M82	0.91693	0.881
9-3-2/M82	1.26277	0.191

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.91457
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86822	0.418
IL12-4/WTpooled	0.85636	0.71
IL1-4/WTpooled	1.07152
WT/WTpooled	0.79923	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	0.62565	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92671	1
DC3000/delta hrp 6h	0.48398
DC3000/delta hrp 12h	1.08937	1
DC3000/delta hrp 24h	0.98403	0.945

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.77923	0.273
DC3000 delta B/DC3000 delta AB	0.87331	0.125

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06728	1
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	0.98221	1
Var 0h	1.27316	0.782
Var 12h I row2-row1	1.13443	0.473
Var 12h NI row2-row1	0.87881	0.443
Var 36h I row2-row1	1.01238	1
Var 36h NI row2-row1	1.19008	1
Var 60h I row2-row1	1.98108	1
Var 60h NI row2-row1	1.24589	0.904
Time course 0hI-0hNI	1.0076	0.852
Time course 12hI-12hNI	0.83876	0.061
Time course 36hI-36hNI	0.69317	0.027
Time course 60hI-60hNI	0.58293	0.007

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)	0.81422	0.391
transgenic ySAMdc/azygous control (breaker)	1.32609	0.248
transgenic ySAMdc/azygous control (red)	0.99793	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04846	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87552	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26889	0.105
Manapal/WT (break)	1.03508	1
Manapal/WT (red)	1.30014	0.222