Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.4.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29298	0.646
27DAP/17DAP	1.49784	0.686
39DAP/27DAP	3.31374	0.021
41DAP/39DAP	2.23578	0.108
42DAP/41DAP	4.26504	0.021
43DAP/42DAP	2.11844	0.816
47DAP/43DAP	1.09837	1
52DAP/47DAP	0.49704	0.057
57DAP/52DAP	1.48148	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77672	0.101
17DAP/reference	0.48226	0.007
27DAP/reference	0.74573	0.048
39DAP/reference	1.70442	0.514
41DAP/reference	1.25423	0.111
42DAP/reference	6.82419	0.001
43DAP/reference	4.97314	0.006
47DAP/reference	4.29445	0.001
52DAP/reference	1.81772	0.007
57DAP/reference	3.62871	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88985	0.277
27DAP/17DAP	0.87741	0.684
39DAP/27DAP	2.31837	0.034
41DAP/39DAP	0.39287	0.013
42DAP/41DAP	1.98441	0.013
43DAP/42DAP	3.53271	0.013
47DAP/43DAP	0.86453	0.506
52DAP/47DAP	0.94288	0.884
57DAP/52DAP	1.77087	0.039
57DAP/7DAP	3.66517	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80313	0.146
17DAP/reference	0.72146	0.108
27DAP/reference	0.80687	0.012
39DAP/reference	0.98207	0.552
41DAP/reference	1.05793	0.741
42DAP/reference	1.04226	1
43DAP/reference	0.85014	0.11
47DAP/reference	1.70795	0.077
52DAP/reference	0.98433	0.523
57DAP/reference	0.91232	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68821	0.093
17DAP/reference	0.78064	0.116
27DAP/reference	0.68616	0.067
39DAP/reference	0.49271	0.011
41DAP/reference	0.54557	0.009
42DAP/reference	0.65753	0.016
43DAP/reference	0.9402	0.336
47DAP/reference	0.88323	0.214
52DAP/reference	0.43364	0.004
57DAP/reference	0.67264	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84727	0.23
17DAP/reference	0.72986	0.328
27DAP/reference	0.78897	0.465
39DAP/reference	0.81354	0.271
41DAP/reference	0.94723	0.512
42DAP/reference	1.96648	0.184
43DAP/reference	4.27799	0.022
47DAP/reference	3.42466	0.005
52DAP/reference	2.30353	0.09
57DAP/reference	1.51987	0.102

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00697	1
26DAP/20DAP	0.93123	0.512
34DAP/26DAP	0.99336	1
51DAP/34DAP	1.07321	0.706
52DAP/51DAP	0.86718	1
53DAP/52DAP	0.98813	0.876
55DAP/53DAP	0.77856	0.325
57DAP/55DAP	1.29185	0.559
62DAP/57DAP	1.20723	0.868
68DAP/62DAP	0.74764	0.429
68DAP/14DAP	0.80604	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	18.1786	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.25566	N/A
Mature Green Tomato/Ripe Tomato	0.17033	0.017
Immature Eggplant/Mature Eggplant	4.27097	N/A
Ripe Pepper/Ripe Tomato	0.1841	0.293
Mature Eggplant/Ripe Tomato	0.04451	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07672	0.877
1-1-2/M82	1.17428	1
12-2/M82	0.96452	0.955
12-4/M82	1.28134	1
1-3/M82	2.88578	0.248
2-1-1/M82	0.85765	0.565
2-1/M82	0.94702	1
2-6/M82	0.88458	1
3-2/M82	1.13836	0.84
4-1-1/M82	0.87521	1
4-1/M82	1.07951	1
4-3-2/M82	1.08953	1
4-3/M82	0.97666	1
5-3/M82	0.97075	1
6-2/M82	0.97703	1
6-3/M82	1.05765	1
7-1/M82	1.04115	0.598
7-2/M82	0.91212	N/A
9-3-2/M82	0.49501	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77411	0.243
IL2-6/WTpooled	0.91104	1
IL7-5/WTpooled	0.52139	N/A
IL7-3/WTpooled	0.92214	1
IL12-4/WTpooled	1.02874	0.839
IL1-4/WTpooled	0.80961	0.699
WT/WTpooled	1.06355	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	1.01709	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05011	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.07871	1
DC3000/delta hrp 24h	0.71941	0.042

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94674	1
DC3000 delta B/DC3000 delta AB	0.67602	0.055

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	1.05024	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96004	1
Var 0h	1.00868	1
Var 12h I row2-row1	0.91626	0.363
Var 12h NI row2-row1	0.90382	0.488
Var 36h I row2-row1	1.04382	0.742
Var 36h NI row2-row1	0.90361	0.645
Var 60h I row2-row1	0.98053	0.952
Var 60h NI row2-row1	0.80718	0.866
Time course 0hI-0hNI	1.02635	0.852
Time course 12hI-12hNI	0.92602	0.393
Time course 36hI-36hNI	0.97872	0.54
Time course 60hI-60hNI	0.84725	0.015

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)	0.54432	0.246
transgenic ySAMdc/azygous control (breaker)	0.9819	1
transgenic ySAMdc/azygous control (red)	1.00737	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.53624	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01423	1
Manapal/WT (break)	1.50228	0.126
Manapal/WT (red)	0.95109	0.728