Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.11.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93868	0.558
27DAP/17DAP	1.0486	1
39DAP/27DAP	0.87816	0.522
41DAP/39DAP	1.49616	0.261
42DAP/41DAP	1.05166	1
43DAP/42DAP	0.84975	0.583
47DAP/43DAP	0.98564	0.902
52DAP/47DAP	1.58904	0.374
57DAP/52DAP	0.91455	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94949	0.162
17DAP/reference	1.01742	0.874
27DAP/reference	1.04055	0.252
39DAP/reference	1.03853	0.57
41DAP/reference	1.10177	0.073
42DAP/reference	0.94241	0.081
43DAP/reference	1.02168	0.758
47DAP/reference	1.002	1
52DAP/reference	0.89469	0.026
57DAP/reference	0.91316	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07864	0.164
27DAP/17DAP	0.95452	0.684
39DAP/27DAP	0.98607	0.943
41DAP/39DAP	0.96462	0.793
42DAP/41DAP	1.11454	0.172
43DAP/42DAP	0.98233	0.684
47DAP/43DAP	0.99575	0.99
52DAP/47DAP	1.2336	0.471
57DAP/52DAP	1.31428	0.106
57DAP/7DAP	1.14153	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91786	0.061
17DAP/reference	0.89937	0.017
27DAP/reference	0.89603	0.012
39DAP/reference	0.9634	0.198
41DAP/reference	0.96464	0.375
42DAP/reference	0.96263	0.289
43DAP/reference	0.92269	0.044
47DAP/reference	0.9445	0.293
52DAP/reference	0.97281	0.332
57DAP/reference	0.93728	0.025

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97147	0.639
17DAP/reference	1.0853	0.036
27DAP/reference	0.89283	0.081
39DAP/reference	0.95606	0.119
41DAP/reference	0.89432	0.124
42DAP/reference	0.95921	0.237
43DAP/reference	1.0623	0.327
47DAP/reference	1.01421	0.775
52DAP/reference	0.93675	0.171
57DAP/reference	1.12933	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93682	0.158
17DAP/reference	0.96581	0.348
27DAP/reference	0.93874	0.089
39DAP/reference	0.93413	0.015
41DAP/reference	0.93563	0.096
42DAP/reference	0.86316	0.02
43DAP/reference	0.88047	0.102
47DAP/reference	0.94248	0.296
52DAP/reference	0.93681	0.342
57DAP/reference	0.76486	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02835	0.945
26DAP/20DAP	1.187	0.524
34DAP/26DAP	1.18038	0.819
51DAP/34DAP	0.97609	0.807
52DAP/51DAP	1.57743	0.099
53DAP/52DAP	0.94254
55DAP/53DAP	1.11761	0.422
57DAP/55DAP	0.73164	0.138
62DAP/57DAP	1.20652	0.081
68DAP/62DAP	1.5171	0.178
68DAP/14DAP	1.00892	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.63839	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.65203
Mature Green Tomato/Ripe Tomato	0.74349	0.036
Immature Eggplant/Mature Eggplant	1.12728
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.90922

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92216	0.944
1-1-2/M82	0.93831	1
12-2/M82	0.97953	0.955
12-4/M82	1.03143	1
1-3/M82	0.85617
2-1-1/M82	0.97586
2-1/M82	1.25827
2-6/M82	0.97526	1
3-2/M82	0.9595
4-1-1/M82	0.93213	1
4-1/M82	0.82009	0.737
4-3-2/M82	0.99932	1
4-3/M82	1.03432	1
5-3/M82	0.99957	1
6-2/M82	1.04256	1
6-3/M82	1.07061
7-1/M82	1.00921	1
7-2/M82	0.88316	0.553
9-3-2/M82	0.97402	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86644	1
IL2-6/WTpooled	1.29615	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.84565	1
IL12-4/WTpooled	0.96437	1
IL1-4/WTpooled	0.94795	1
WT/WTpooled	0.90587	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	0.93239	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89046	0.545
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.06244	1
DC3000/delta hrp 24h	1.00995	0.821

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.4732	0.042
DC3000 delta B/DC3000 delta AB	1.5129	0.101

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	0.97749	1
Var 0h	1.20139	0.421
Var 12h I row2-row1	0.90955	0.77
Var 12h NI row2-row1	1.09364	0.649
Var 36h I row2-row1	1.12788	0.742
Var 36h NI row2-row1	1.10794	0.482
Var 60h I row2-row1	0.99692	1
Var 60h NI row2-row1	1.09752	0.904
Time course 0hI-0hNI	0.9504	0.751
Time course 12hI-12hNI	0.98934	0.956
Time course 36hI-36hNI	0.97394	0.524
Time course 60hI-60hNI	1.04169	0.673

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)	2.59091	0.921
transgenic ySAMdc/azygous control (breaker)	1.38407	1
transgenic ySAMdc/azygous control (red)	0.97579	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00404	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69764	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90019	1
Manapal/WT (break)	0.9351	1
Manapal/WT (red)	0.88101	0.36