Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98749	0.867
27DAP/17DAP	0.86837	0.635
39DAP/27DAP	1.0158	1
41DAP/39DAP	0.98849	0.841
42DAP/41DAP	1.1557	0.871
43DAP/42DAP	1.03735	1
47DAP/43DAP	0.96428	0.868
52DAP/47DAP	0.92676	0.752
57DAP/52DAP	0.97236	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99056	0.63
17DAP/reference	1.00533	0.874
27DAP/reference	1.07762	0.184
39DAP/reference	1.03922	0.111
41DAP/reference	1.00262	1
42DAP/reference	0.99021	0.425
43DAP/reference	1.0311	0.36
47DAP/reference	0.99213	0.602
52DAP/reference	0.9237	0.202
57DAP/reference	1.07863	0.366

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1168	0.473
27DAP/17DAP	1.03433	0.924
39DAP/27DAP	0.95061	0.482
41DAP/39DAP	0.93952	0.696
42DAP/41DAP	0.92015	0.529
43DAP/42DAP	1.09956	0.066
47DAP/43DAP	1.00624	0.973
52DAP/47DAP	0.98894	0.935
57DAP/52DAP	0.98738	0.804
57DAP/7DAP	0.92871	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02042	1
17DAP/reference	1.09853	0.084
27DAP/reference	1.06246	0.131
39DAP/reference	1.0956	0.066
41DAP/reference	1.14324	0.136
42DAP/reference	1.12344	0.046
43DAP/reference	1.06186	0.307
47DAP/reference	1.06107	0.514
52DAP/reference	1.13924	0.043
57DAP/reference	1.26442	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92336	0.145
17DAP/reference	0.95102	0.195
27DAP/reference	0.98564	0.598
39DAP/reference	0.99294	0.603
41DAP/reference	0.94989	0.133
42DAP/reference	0.94295	0.189
43DAP/reference	0.93172	0.25
47DAP/reference	0.96526	0.292
52DAP/reference	0.90472	0.034
57DAP/reference	0.9175	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0975	0.287
17DAP/reference	0.99467	0.87
27DAP/reference	1.04104
39DAP/reference	1.1635	0.032
41DAP/reference	1.10784	0.04
42DAP/reference	1.10647	0.408
43DAP/reference	1.08621	0.331
47DAP/reference	1.13135	0.163
52DAP/reference	1.11758	0.517
57DAP/reference	1.45743	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00598	1
26DAP/20DAP	0.98154	1
34DAP/26DAP	1.04599	0.819
51DAP/34DAP	0.93894	0.571
52DAP/51DAP	1.03122	0.776
53DAP/52DAP	0.86619	0.358
55DAP/53DAP	0.94959	0.53
57DAP/55DAP	0.98775	0.927
62DAP/57DAP	1.10846	0.8
68DAP/62DAP	0.99158	0.914
68DAP/14DAP	1.20559	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02099	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.03306	1
Mature Green Tomato/Ripe Tomato	1.36884	0.577
Immature Eggplant/Mature Eggplant	0.73998	0.077
Ripe Pepper/Ripe Tomato	0.83736	0.293
Mature Eggplant/Ripe Tomato	0.70445	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96783	0.944
1-1-2/M82	1.01341	1
12-2/M82	0.94136	0.955
12-4/M82	0.99507	1
1-3/M82	0.96925	1
2-1-1/M82	2.38098	0.764
2-1/M82	0.76684
2-6/M82	1.01119	1
3-2/M82	0.98464	1
4-1-1/M82	1.08743	1
4-1/M82	1.03616	1
4-3-2/M82	N/A	N/A
4-3/M82	0.98025	0.72
5-3/M82	1.04339	0.572
6-2/M82	0.93076	1
6-3/M82	0.8847	1
7-1/M82	0.93607	0.466
7-2/M82	N/A	N/A
9-3-2/M82	0.91239	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08792	0.395
IL7-5/WTpooled	1.18679	1
IL7-3/WTpooled	1.26871
IL12-4/WTpooled	0.8532	0.543
IL1-4/WTpooled	1.06494	1
WT/WTpooled	0.8427	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	0.99545	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02222	0.921
DC3000/delta hrp 6h	0.87859	0.95
DC3000/delta hrp 12h	1.09289	1
DC3000/delta hrp 24h	0.87466	0.313

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76297
DC3000 delta B/DC3000 delta AB	0.76597	0.02

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	0.99112	1
Var 0h	0.96332	1
Var 12h I row2-row1	0.8676	0.357
Var 12h NI row2-row1	0.8834	0.546
Var 36h I row2-row1	1.02939	1
Var 36h NI row2-row1	1.1566	1
Var 60h I row2-row1	1.0104	1
Var 60h NI row2-row1	0.96338	1
Time course 0hI-0hNI	0.95733	0.687
Time course 12hI-12hNI	0.97485	0.776
Time course 36hI-36hNI	0.93618	0.373
Time course 60hI-60hNI	0.34141	0.005

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)	1.00658	0.921
transgenic ySAMdc/azygous control (breaker)	1.38785	0.172
transgenic ySAMdc/azygous control (red)	1.46187	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05496	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10896	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.84068	0.084
Manapal/WT (break)	1.65591	0.381
Manapal/WT (red)	3.21519	0.133