Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.13.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.68675	0.048
27DAP/17DAP	1.14768	0.854
39DAP/27DAP	0.80918	0.447
41DAP/39DAP	0.88294	0.555
42DAP/41DAP	0.95158	1
43DAP/42DAP	1.02513	0.937
47DAP/43DAP	1.20161	0.609
52DAP/47DAP	0.80361	0.476
57DAP/52DAP	1.10231	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04331	0.928
17DAP/reference	1.01709	0.528
27DAP/reference	0.97428	0.61
39DAP/reference	0.99049	0.874
41DAP/reference	1.11208	0.122
42DAP/reference	0.89984	0.018
43DAP/reference	0.95676	0.519
47DAP/reference	0.89193	0.023
52DAP/reference	0.91879	0.244
57DAP/reference	1.05746	0.463

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79147	0.08
27DAP/17DAP	1.15967	0.699
39DAP/27DAP	0.96229	0.768
41DAP/39DAP	0.86867	0.567
42DAP/41DAP	1.23699	0.2
43DAP/42DAP	0.95946	0.709
47DAP/43DAP	0.87694	0.239
52DAP/47DAP	1.09587	0.799
57DAP/52DAP	1.08733	0.869
57DAP/7DAP	0.61265

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90445	0.122
17DAP/reference	1.07484	0.754
27DAP/reference	1.12655	0.049
39DAP/reference	0.97527	0.474
41DAP/reference	1.0786	0.977
42DAP/reference	0.99003	0.612
43DAP/reference	1.11057	0.537
47DAP/reference	0.83502	0.057
52DAP/reference	0.89606	0.137
57DAP/reference	0.93251	0.291

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17951	0.424
17DAP/reference	1.01829	0.873
27DAP/reference	1.06261	0.988
39DAP/reference	0.86907	0.168
41DAP/reference	1.11199	0.459
42DAP/reference	0.96433	0.433
43DAP/reference	1.1199	0.835
47DAP/reference	0.86121	0.032
52DAP/reference	1.05279	0.988
57DAP/reference	0.85128	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03671	0.864
17DAP/reference	1.14002	0.412
27DAP/reference	1.12179	0.143
39DAP/reference	1.04327	0.563
41DAP/reference	1.12483	0.621
42DAP/reference	1.09021	0.408
43DAP/reference	0.90494	0.197
47DAP/reference	0.96217	0.409
52DAP/reference	1.34113	0.601
57DAP/reference	1.02116	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87552	1
26DAP/20DAP	0.46838	0.317
34DAP/26DAP	0.84893	0.509
51DAP/34DAP	0.63663	0.065
52DAP/51DAP	0.71138	1
53DAP/52DAP	0.90731	0.776
55DAP/53DAP	0.93245	0.686
57DAP/55DAP	1.19212	1
62DAP/57DAP	0.88552	0.871
68DAP/62DAP	1.05267	0.872
68DAP/14DAP	0.7055	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70735	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.7444	0.23
Mature Green Tomato/Ripe Tomato	2.64018	0.018
Immature Eggplant/Mature Eggplant	0.61793	0.062
Ripe Pepper/Ripe Tomato	3.58055	1
Mature Eggplant/Ripe Tomato	4.95768	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18612	0.591
1-1-2/M82	1.03724	1
12-2/M82	1.04089	1
12-4/M82	0.89201
1-3/M82	0.81443	0.441
2-1-1/M82	0.94006
2-1/M82	N/A	N/A
2-6/M82	0.98973	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.13834
4-3/M82	0.62061
5-3/M82	0.93985	1
6-2/M82	0.73483
6-3/M82	1.06564	1
7-1/M82	N/A	N/A
7-2/M82	1.30267	0.324
9-3-2/M82	1.41598

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02687	1
IL2-6/WTpooled	0.9392	1
IL7-5/WTpooled	1.18892	0.792
IL7-3/WTpooled	0.98151	1
IL12-4/WTpooled	1.14309	0.737
IL1-4/WTpooled	1.08999	1
WT/WTpooled	1.00434	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	1.0541	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02486	0.921
DC3000/delta hrp 6h	1.1523	1
DC3000/delta hrp 12h	0.82001	1
DC3000/delta hrp 24h	0.86708	0.186

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44642	0.036
DC3000 delta B/DC3000 delta AB	1.17514	0.625

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.73007	0.265
Exp 36h	0.59871	0.393
Exp 60h	0.57037	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03699	1
Var 0h	1.25932	0.259
Var 12h I row2-row1	0.92943	0.357
Var 12h NI row2-row1	0.91338	0.82
Var 36h I row2-row1	0.72829	0.805
Var 36h NI row2-row1	1.06929	1
Var 60h I row2-row1	0.91786	0.306
Var 60h NI row2-row1	1.34144	0.631
Time course 0hI-0hNI	0.96966	0.863
Time course 12hI-12hNI	0.95695	0.739
Time course 36hI-36hNI	0.74324	0.023
Time course 60hI-60hNI	0.37262	0.006

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)	0.92231	0.529
transgenic ySAMdc/azygous control (breaker)	1.90245	0.166
transgenic ySAMdc/azygous control (red)	1.13669	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92498	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.17522	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.10521	1
Manapal/WT (break)	1.71698	0.183
Manapal/WT (red)	0.94411	0.274