Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.1.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03934	0.863
27DAP/17DAP	1.02991	0.92
39DAP/27DAP	1.24999	0.718
41DAP/39DAP	0.85379	0.392
42DAP/41DAP	1.24283	0.709
43DAP/42DAP	1.09944	1
47DAP/43DAP	1.07366	0.756
52DAP/47DAP	0.95345	0.765
57DAP/52DAP	1.28539	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09038	0.303
17DAP/reference	0.95471	0.393
27DAP/reference	0.97638	0.654
39DAP/reference	1.11322	0.224
41DAP/reference	0.97078	0.542
42DAP/reference	1.05667	0.299
43DAP/reference	1.04832	0.269
47DAP/reference	0.98306	0.392
52DAP/reference	1.064	0.217
57DAP/reference	1.04455	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96334	0.578
27DAP/17DAP	0.8834	0.537
39DAP/27DAP	0.87466	0.377
41DAP/39DAP	0.9094	0.696
42DAP/41DAP	1.01686	0.887
43DAP/42DAP	1.00795	1
47DAP/43DAP	0.91586	0.499
52DAP/47DAP	1.04408	0.844
57DAP/52DAP	0.9022	0.498
57DAP/7DAP	0.76549	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99635	0.682
17DAP/reference	0.90049	0.192
27DAP/reference	1.0974	0.551
39DAP/reference	1.14075	0.252
41DAP/reference	1.08278	0.507
42DAP/reference	1.15271	0.534
43DAP/reference	0.93042	0.151
47DAP/reference	1.04031	0.761
52DAP/reference	1.05514	0.428
57DAP/reference	1.00254	0.719

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14803	0.177
17DAP/reference	1.08702	0.303
27DAP/reference	1.07779	0.345
39DAP/reference	0.94261	0.168
41DAP/reference	1.07575	0.491
42DAP/reference	0.99858	0.655
43DAP/reference	1.09435	0.268
47DAP/reference	1.05016	0.527
52DAP/reference	1.01004	0.761
57DAP/reference	0.92266	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00271	0.75
17DAP/reference	1.05781	0.738
27DAP/reference	1.04689	0.967
39DAP/reference	1.04228	0.496
41DAP/reference	1.15377	0.319
42DAP/reference	1.12295	0.294
43DAP/reference	1.10114	0.275
47DAP/reference	0.96191	0.409
52DAP/reference	0.8522	0.197
57DAP/reference	1.12191	0.147

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90631	0.915
26DAP/20DAP	0.98611	1
34DAP/26DAP	1.63753	0.819
51DAP/34DAP	0.8886	0.286
52DAP/51DAP	0.81187	1
53DAP/52DAP	1.05059	0.921
55DAP/53DAP	1.07584	0.911
57DAP/55DAP	1.15538	0.71
62DAP/57DAP	1.22182
68DAP/62DAP	1.05176	0.984
68DAP/14DAP	0.94291	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.48845	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.17429	0.331
Immature Eggplant/Mature Eggplant	1.07617	0.633
Ripe Pepper/Ripe Tomato	0.50267	0.293
Mature Eggplant/Ripe Tomato	0.86409	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26351	0.742
1-1-2/M82	1.11969	1
12-2/M82	0.95669	0.955
12-4/M82	1.01893	1
1-3/M82	0.89303	0.501
2-1-1/M82	0.70465	0.465
2-1/M82	0.58701
2-6/M82	1.03296	1
3-2/M82	0.81311
4-1-1/M82	0.78682	0.926
4-1/M82	1.23002	0.344
4-3-2/M82	1.19804	0.508
4-3/M82	1.2427	0.268
5-3/M82	1.00129	1
6-2/M82	0.87038	1
6-3/M82	0.92864	1
7-1/M82	0.60907
7-2/M82	0.88734	0.796
9-3-2/M82	1.07615	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.68865	0.243
IL2-6/WTpooled	0.90453	1
IL7-5/WTpooled	1.02199	1
IL7-3/WTpooled	0.76808	0.418
IL12-4/WTpooled	1.15543	0.839
IL1-4/WTpooled	1.05832	1
WT/WTpooled	1.05576	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	1.10926	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12579	0.921
DC3000/delta hrp 6h	1.00318	0.95
DC3000/delta hrp 12h	0.99065	1
DC3000/delta hrp 24h	1.0654	0.383

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	1.21979	0.368

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05212	1
Exp 36h	1.04238	1
Exp 60h	1.08394	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99542	1
Var 0h	1.02359	1
Var 12h I row2-row1	0.80875	0.344
Var 12h NI row2-row1	0.87424	0.82
Var 36h I row2-row1	0.97556	1
Var 36h NI row2-row1	2.03132	1
Var 60h I row2-row1	0.98004	0.832
Var 60h NI row2-row1	0.83184	0.69
Time course 0hI-0hNI	0.93102	0.522
Time course 12hI-12hNI	1.04315	0.762
Time course 36hI-36hNI	1.20519	0.006
Time course 60hI-60hNI	1.9848	0.008

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)	1.02011	0.798
transgenic ySAMdc/azygous control (breaker)	1.04091	1
transgenic ySAMdc/azygous control (red)	0.94214	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05817	0.194

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86093	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89862	1
Manapal/WT (break)	0.86309	1
Manapal/WT (red)	0.89772	0.424