Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17975	0.403
27DAP/17DAP	1.00114	1
39DAP/27DAP	1.4867	0.265
41DAP/39DAP	0.90434	0.597
42DAP/41DAP	1.31833	0.751
43DAP/42DAP	0.98733	0.925
47DAP/43DAP	1.23169	0.756
52DAP/47DAP	0.93742	0.742
57DAP/52DAP	0.98821	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92447	0.308
17DAP/reference	0.99189	0.819
27DAP/reference	1.04301	0.721
39DAP/reference	1.0152	0.786
41DAP/reference	0.95064	0.542
42DAP/reference	0.88219	0.008
43DAP/reference	0.97441	0.691
47DAP/reference	0.85499	0.005
52DAP/reference	0.79313	0.093
57DAP/reference	0.77068	0.065

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37905	0.036
27DAP/17DAP	1.01759	0.995
39DAP/27DAP	1.10734	0.534
41DAP/39DAP	1.21067	0.063
42DAP/41DAP	0.94429	0.595
43DAP/42DAP	0.8229	0.085
47DAP/43DAP	1.16821	0.221
52DAP/47DAP	1.26078	0.367
57DAP/52DAP	1.01799	0.857
57DAP/7DAP	1.318	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83851	0.076
17DAP/reference	0.81498	0.031
27DAP/reference	1.25864	0.371
39DAP/reference	0.81846	0.17
41DAP/reference	1.22087	0.291
42DAP/reference	1.23514	0.405
43DAP/reference	1.14057	0.637
47DAP/reference	0.95485	0.504
52DAP/reference	1.19529	0.081
57DAP/reference	1.0156	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00933	0.979
17DAP/reference	0.97442	0.434
27DAP/reference	0.86285	0.115
39DAP/reference	0.81604	0.099
41DAP/reference	0.70595	0.012
42DAP/reference	0.76471	0.089
43DAP/reference	0.88588	0.186
47DAP/reference	0.81768	0.029
52DAP/reference	0.9152	0.131
57DAP/reference	1.10968	0.437

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04787	0.827
17DAP/reference	0.98669	0.792
27DAP/reference	1.10959	0.749
39DAP/reference	1.40416	0.67
41DAP/reference	1.34265	0.036
42DAP/reference	0.87845	0.361
43DAP/reference	1.1385	1
47DAP/reference	0.88642	0.296
52DAP/reference	1.63045	0.205
57DAP/reference	0.63815	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08389	0.916
26DAP/20DAP	1.06873	1
34DAP/26DAP	1.0212	1
51DAP/34DAP	1.87551	0.032
52DAP/51DAP	0.94137	1
53DAP/52DAP	1.07156	1
55DAP/53DAP	0.97063	0.775
57DAP/55DAP	1.21706	0.643
62DAP/57DAP	1.38531	0.021
68DAP/62DAP	1.01566	0.977
68DAP/14DAP	0.74532	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92004	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.82643	0.038
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.86926	0.258
Mature Eggplant/Ripe Tomato	0.61776	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2487	0.505
1-1-2/M82	1.23106	1
12-2/M82	1.01521	1
12-4/M82	0.95757	1
1-3/M82	2.00111
2-1-1/M82	0.83083	0.565
2-1/M82	0.65138	0.345
2-6/M82	0.97877	1
3-2/M82	1.21231	0.717
4-1-1/M82	0.87031	1
4-1/M82	1.27452	0.397
4-3-2/M82	1.25878	0.284
4-3/M82	1.53855	0.268
5-3/M82	1.0925	1
6-2/M82	1.56638	1
6-3/M82	1.27087	1
7-1/M82	0.8911	0.509
7-2/M82	0.90895	0.599
9-3-2/M82	0.99789	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86407	1
IL2-6/WTpooled	1.09678	0.659
IL7-5/WTpooled	1.78338
IL7-3/WTpooled	1.05958	1
IL12-4/WTpooled	1.05914	0.595
IL1-4/WTpooled	0.92219	0.834
WT/WTpooled	0.94523	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	1.17132	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07939	0.846
DC3000/delta hrp 6h	0.62847	0.95
DC3000/delta hrp 12h	0.9587	1
DC3000/delta hrp 24h	1.08336	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.69582	0.087
DC3000 delta B/DC3000 delta AB	1.40152	0.208

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.35135	1
Exp 36h	N/A	N/A
Exp 60h	0.77319	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06432	1
Var 0h	0.88167	0.933
Var 12h I row2-row1	1.10112	0.254
Var 12h NI row2-row1	1.19991	0.649
Var 36h I row2-row1	1.17311	0.908
Var 36h NI row2-row1	0.8219	0.522
Var 60h I row2-row1	0.71117	0.306
Var 60h NI row2-row1	0.76337	0.408
Time course 0hI-0hNI	1.0204	0.833
Time course 12hI-12hNI	1.32528	0.013
Time course 36hI-36hNI	2.53341	0.005
Time course 60hI-60hNI	5.25255	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)	1.0306	0.431
transgenic ySAMdc/azygous control (breaker)	0.9429	0.251
transgenic ySAMdc/azygous control (red)	0.99832	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99513	0.651

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27691	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91643	1
Manapal/WT (break)	0.93093	1
Manapal/WT (red)	1.1873	0.413