Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82218	0.331
27DAP/17DAP	1.23815	0.809
39DAP/27DAP	0.97804	0.769
41DAP/39DAP	1.15414	0.663
42DAP/41DAP	1.28658	0.404
43DAP/42DAP	1.04351	1
47DAP/43DAP	0.97101	0.864
52DAP/47DAP	0.8493	0.607
57DAP/52DAP	0.92993	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88059	0.071
17DAP/reference	1.08246	0.675
27DAP/reference	1.06237	0.435
39DAP/reference	1.03227	0.734
41DAP/reference	1.01775	1
42DAP/reference	0.88024	0.007
43DAP/reference	1.07642	0.306
47DAP/reference	0.86613	0.065
52DAP/reference	1.02699	0.991
57DAP/reference	1.03367	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20707	0.899
27DAP/17DAP	1.0738	0.885
39DAP/27DAP	1.21536	0.253
41DAP/39DAP	1.00847	1
42DAP/41DAP	0.94187	0.612
43DAP/42DAP	1.15297	0.413
47DAP/43DAP	1.11949	0.88
52DAP/47DAP	0.85729	0.378
57DAP/52DAP	1.17855	0.346
57DAP/7DAP	0.75878	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17848	0.189
17DAP/reference	1.00051	0.693
27DAP/reference	1.05307	0.551
39DAP/reference	0.81933	0.073
41DAP/reference	1.06415	0.491
42DAP/reference	0.95596	0.436
43DAP/reference	1.07015	0.457
47DAP/reference	1.00715	1
52DAP/reference	0.98615	0.571
57DAP/reference	0.97783	0.53

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84989	0.1
17DAP/reference	0.89557	0.182
27DAP/reference	0.92646	0.269
39DAP/reference	0.9195	0.235
41DAP/reference	0.88549	0.16
42DAP/reference	0.91532	0.189
43DAP/reference	1.24793	0.441
47DAP/reference	1.02187	1
52DAP/reference	0.97845	0.5
57DAP/reference	1.0351	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23636	0.041
17DAP/reference	1.07348	0.578
27DAP/reference	1.1183	0.721
39DAP/reference	1.00215	0.819
41DAP/reference	1.00081	0.826
42DAP/reference	1.11366	0.68
43DAP/reference	0.94994	0.449
47DAP/reference	1.1353	0.443
52DAP/reference	1.84502	0.398
57DAP/reference	1.04852	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95278	1
26DAP/20DAP	0.85537	1
34DAP/26DAP	1.06137	1
51DAP/34DAP	1.464	0.105
52DAP/51DAP	0.96406	1
53DAP/52DAP	1.1824	0.428
55DAP/53DAP	1.00299	0.951
57DAP/55DAP	1.24787	0.364
62DAP/57DAP	0.89524	0.871
68DAP/62DAP	0.74977	0.464
68DAP/14DAP	1.69255	0.03

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31031	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.73219	0.021
Immature Eggplant/Mature Eggplant	2.09929	0.052
Ripe Pepper/Ripe Tomato	0.40366	0.224
Mature Eggplant/Ripe Tomato	0.77611	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16564	0.877
1-1-2/M82	1.37855	1
12-2/M82	1.28691	1
12-4/M82	1.00072	1
1-3/M82	1.85825
2-1-1/M82	0.86228	0.465
2-1/M82	0.89603	1
2-6/M82	0.76061	0.501
3-2/M82	1.51756	0.461
4-1-1/M82	0.86518	1
4-1/M82	N/A	N/A
4-3-2/M82	1.14953	1
4-3/M82	0.97407	1
5-3/M82	0.8657	0.642
6-2/M82	1.38513	1
6-3/M82	1.26236	1
7-1/M82	0.99262
7-2/M82	1.51732
9-3-2/M82	1.17456	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.77545
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9853	1
IL12-4/WTpooled	0.83571	0.71
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.02345	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	1.18989	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03017	0.914
DC3000/delta hrp 6h	0.86199	0.95
DC3000/delta hrp 12h	0.95628	1
DC3000/delta hrp 24h	3.47518	0.019

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	1.99717

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.54338	1
Exp 60h	1.28852	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99115	1
Var 0h	0.66732	0.933
Var 12h I row2-row1	0.95439	0.77
Var 12h NI row2-row1	1.18884	0.649
Var 36h I row2-row1	1.45855	0.339
Var 36h NI row2-row1	0.58003	0.478
Var 60h I row2-row1	0.75069	0.306
Var 60h NI row2-row1	0.77479	0.408
Time course 0hI-0hNI	0.95509	0.755
Time course 12hI-12hNI	1.13066	0.213
Time course 36hI-36hNI	2.21471	0.004
Time course 60hI-60hNI	7.45771	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)	1.25161	0.272
transgenic ySAMdc/azygous control (breaker)	0.90203	0.251
transgenic ySAMdc/azygous control (red)	0.87948	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96769	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37308	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86172	0.172
Manapal/WT (break)	0.91121	1
Manapal/WT (red)	0.94048	0.36