Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.13.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90765	0.558
27DAP/17DAP	1.22195	0.866
39DAP/27DAP	0.78759	0.474
41DAP/39DAP	1.94072	0.387
42DAP/41DAP	1.22866	1
43DAP/42DAP	0.99103	0.912
47DAP/43DAP	1.03229	0.687
52DAP/47DAP	2.11784	0.252
57DAP/52DAP	0.72155	0.711

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9727	0.526
17DAP/reference	0.99118	0.819
27DAP/reference	0.92468	0.119
39DAP/reference	1.00281	1
41DAP/reference	1.00048	1
42DAP/reference	0.95852	0.111
43DAP/reference	0.95777	0.273
47DAP/reference	0.93798	0.116
52DAP/reference	0.87526	0.024
57DAP/reference	0.91582	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92625	0.388
27DAP/17DAP	0.96104	0.854
39DAP/27DAP	1.10569	0.519
41DAP/39DAP	1.14192	0.837
42DAP/41DAP	0.95553	0.67
43DAP/42DAP	1.08351	0.478
47DAP/43DAP	1.04262	0.93
52DAP/47DAP	0.94664	0.797
57DAP/52DAP	0.93312	0.572
57DAP/7DAP	1.10935	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91852	0.296
17DAP/reference	0.94829	0.22
27DAP/reference	0.97962	0.402
39DAP/reference	0.86759	0.025
41DAP/reference	0.9606	0.326
42DAP/reference	0.96766	0.189
43DAP/reference	0.85585	0.025
47DAP/reference	1.06636	0.965
52DAP/reference	0.85719	0.083
57DAP/reference	0.77263	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04167	0.477
17DAP/reference	1.08126	0.406
27DAP/reference	1.20872	0.254
39DAP/reference	0.9112	0.202
41DAP/reference	0.92962	0.127
42DAP/reference	0.99241	0.594
43DAP/reference	1.23069	0.049
47DAP/reference	1.05331	0.332
52DAP/reference	1.02783	0.417
57DAP/reference	1.16783	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94324	0.23
17DAP/reference	1.01727	0.854
27DAP/reference	1.0216	0.672
39DAP/reference	0.98066	0.544
41DAP/reference	1.26766	0.369
42DAP/reference	1.05487	0.775
43DAP/reference	0.89639	0.179
47DAP/reference	1.1009	0.055
52DAP/reference	0.92358	0.327
57DAP/reference	0.87473	0.065

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06762	0.966
26DAP/20DAP	0.92233	0.317
34DAP/26DAP	0.98246	0.98
51DAP/34DAP	0.99701	0.957
52DAP/51DAP	0.98033	1
53DAP/52DAP	1.00237	1
55DAP/53DAP	1.01466	0.955
57DAP/55DAP	1.13557	0.694
62DAP/57DAP	1.03049	1
68DAP/62DAP	0.85796	0.195
68DAP/14DAP	0.91692	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.48977	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50084	0.094
Mature Green Tomato/Ripe Tomato	0.8252	0.522
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	6.72664	0.258
Mature Eggplant/Ripe Tomato	1.34725

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.054	1
1-1-2/M82	1.06079
12-2/M82	0.94426
12-4/M82	1.25037	1
1-3/M82	0.81402	0.378
2-1-1/M82	1.14477
2-1/M82	0.96154
2-6/M82	1.19476	0.452
3-2/M82	N/A	N/A
4-1-1/M82	1.03752	1
4-1/M82	1.07098	1
4-3-2/M82	1.04309
4-3/M82	N/A	N/A
5-3/M82	0.93565	1
6-2/M82	0.77128	1
6-3/M82	0.88437	1
7-1/M82	0.89914
7-2/M82	1.07759	1
9-3-2/M82	0.98179

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14962	0.277
IL2-6/WTpooled	0.95714	1
IL7-5/WTpooled	0.7566	1
IL7-3/WTpooled	1.0733	1
IL12-4/WTpooled	0.929	1
IL1-4/WTpooled	0.96347	0.422
WT/WTpooled	0.98003	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	1.01603	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94066	1
DC3000/delta hrp 6h	1.08213	1
DC3000/delta hrp 12h	1.11221	1
DC3000/delta hrp 24h	1.04296	0.604

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	1.00776	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.9105	0.943
Exp 60h	0.94012	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94578	1
Var 0h	1.15069	0.421
Var 12h I row2-row1	1.05162	0.692
Var 12h NI row2-row1	0.76703	0.494
Var 36h I row2-row1	0.91027	0.805
Var 36h NI row2-row1	0.86469	0.645
Var 60h I row2-row1	1.24195	0.562
Var 60h NI row2-row1	1.1672	0.904
Time course 0hI-0hNI	1.07125	0.662
Time course 12hI-12hNI	1.02048	0.811
Time course 36hI-36hNI	0.998	0.798
Time course 60hI-60hNI	0.96442	0.646

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)	1.06484	0.286
transgenic ySAMdc/azygous control (breaker)	1.17018	0.165
transgenic ySAMdc/azygous control (red)	1.00622	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98845	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13856	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08445	0.307
Manapal/WT (break)	1.13741	0.381
Manapal/WT (red)	0.91856	0.315