Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.8.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50773	0.162
27DAP/17DAP	1.02009	0.92
39DAP/27DAP	0.8438	0.522
41DAP/39DAP	1.0018	0.879
42DAP/41DAP	0.96634	1
43DAP/42DAP	1.08321	0.937
47DAP/43DAP	1.20359	0.442
52DAP/47DAP	0.79775	0.502
57DAP/52DAP	0.83046	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90634	0.149
17DAP/reference	1.15606	0.023
27DAP/reference	1.08157	0.175
39DAP/reference	1.07988	0.311
41DAP/reference	1.11712	0.338
42DAP/reference	0.89817	0.099
43DAP/reference	0.99412	0.84
47DAP/reference	0.97773	0.418
52DAP/reference	0.76896	0.073
57DAP/reference	0.8656	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.50194	0.05
27DAP/17DAP	0.91988	0.648
39DAP/27DAP	0.86181	0.361
41DAP/39DAP	0.9404	0.849
42DAP/41DAP	0.99464	0.882
43DAP/42DAP	0.86464	0.076
47DAP/43DAP	1.05111	0.844
52DAP/47DAP	1.11683	0.649
57DAP/52DAP	0.92226	0.445
57DAP/7DAP	2.02736	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85308	0.074
17DAP/reference	1.07289	0.574
27DAP/reference	1.04522	1
39DAP/reference	1.20178	0.046
41DAP/reference	1.08278	0.507
42DAP/reference	1.43477	0.1
43DAP/reference	1.08618	0.873
47DAP/reference	0.80677	0.222
52DAP/reference	0.9583	0.363
57DAP/reference	1.15042	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01252	1
17DAP/reference	1.07612	0.136
27DAP/reference	0.8839	0.22
39DAP/reference	0.92073	0.265
41DAP/reference	0.86377	0.014
42DAP/reference	0.85194	0.081
43DAP/reference	1.15419	0.226
47DAP/reference	0.97634	0.39
52DAP/reference	0.96033	0.351
57DAP/reference	1.36651	0.039

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90439	0.214
17DAP/reference	1.04991	0.775
27DAP/reference	1.04085	0.749
39DAP/reference	0.98071	0.591
41DAP/reference	0.99504	0.754
42DAP/reference	0.79042	0.071
43DAP/reference	0.82925	0.092
47DAP/reference	0.97609	0.478
52DAP/reference	0.94419	0.433
57DAP/reference	0.64837	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13181	0.85
26DAP/20DAP	1.30722	0.798
34DAP/26DAP	0.71967	0.131
51DAP/34DAP	0.89286	0.555
52DAP/51DAP	1.08087	0.492
53DAP/52DAP	0.87848	0.498
55DAP/53DAP	1.10797	0.82
57DAP/55DAP	1.21121	0.805
62DAP/57DAP	1.09918	1
68DAP/62DAP	0.82628	0.7
68DAP/14DAP	1.01559	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.11756	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.55287	0.058
Mature Green Tomato/Ripe Tomato	5.62934	0.237
Immature Eggplant/Mature Eggplant	1.51655	0.239
Ripe Pepper/Ripe Tomato	2.06418	1
Mature Eggplant/Ripe Tomato	2.12389

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.183	1
12-2/M82	N/A	N/A
12-4/M82	0.82707	0.619
1-3/M82	0.72293
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.79468
4-1-1/M82	N/A	N/A
4-1/M82	0.98013	1
4-3-2/M82	0.92991	0.487
4-3/M82	N/A	N/A
5-3/M82	0.72072	0.642
6-2/M82	N/A	N/A
6-3/M82	0.99925
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.91647	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85859
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.76669
IL1-4/WTpooled	1.17262	1
WT/WTpooled	0.8889

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	1.13902	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9143	1
DC3000/delta hrp 6h	0.86973	0.95
DC3000/delta hrp 12h	1.11554	1
DC3000/delta hrp 24h	0.95918	0.725

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	0.83855

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09499	1
Exp 36h	1.72198	1
Exp 60h	1.05122	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03925	1
Var 0h	1.13242	0.782
Var 12h I row2-row1	1.02037	1
Var 12h NI row2-row1	0.9158	0.466
Var 36h I row2-row1	0.93594	0.805
Var 36h NI row2-row1	0.84921	0.61
Var 60h I row2-row1	1.02323	1
Var 60h NI row2-row1	0.98864	1
Time course 0hI-0hNI	1.06719	0.603
Time course 12hI-12hNI	0.99495	1
Time course 36hI-36hNI	1.00101	0.826
Time course 60hI-60hNI	1.04916	1

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)	1.15662	0.212
transgenic ySAMdc/azygous control (breaker)	0.7041	0.131
transgenic ySAMdc/azygous control (red)	1.06145	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01423	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.3703	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64189	0.172
Manapal/WT (break)	0.98211	1
Manapal/WT (red)	1.23123	0.413