Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.17.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44453	0.176
27DAP/17DAP	0.93494	0.902
39DAP/27DAP	1.01686	0.798
41DAP/39DAP	1.11792	0.914
42DAP/41DAP	0.95267	1
43DAP/42DAP	1.85012	0.207
47DAP/43DAP	0.61483	0.084
52DAP/47DAP	1.0817	0.953
57DAP/52DAP	0.93744	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84261	0.115
17DAP/reference	0.92673	0.208
27DAP/reference	0.89316	0.163
39DAP/reference	1.03559	1
41DAP/reference	1.11156	0.421
42DAP/reference	0.96508	0.233
43DAP/reference	0.77532	0.024
47DAP/reference	1.01855	1
52DAP/reference	1.04427	1
57DAP/reference	0.97941	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14662	1
27DAP/17DAP	0.99985	0.943
39DAP/27DAP	1.10671	0.663
41DAP/39DAP	0.99002	0.98
42DAP/41DAP	0.79953	0.122
43DAP/42DAP	1.25794	0.324
47DAP/43DAP	1.1641	0.848
52DAP/47DAP	1.29432	0.463
57DAP/52DAP	1.05586	0.783
57DAP/7DAP	0.92628

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8913	0.129
17DAP/reference	1.1656	0.328
27DAP/reference	1.05288	0.551
39DAP/reference	1.49254	0.027
41DAP/reference	1.41504	0.033
42DAP/reference	1.20007	0.021
43DAP/reference	1.26546	0.066
47DAP/reference	0.99003	1
52DAP/reference	1.21939	0.033
57DAP/reference	1.15066	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01209	0.951
17DAP/reference	1.1502	0.257
27DAP/reference	1.04219	1
39DAP/reference	1.02323	0.603
41DAP/reference	1.33882	0.109
42DAP/reference	1.27349	0.038
43DAP/reference	1.15704	0.713
47DAP/reference	1.12441	0.205
52DAP/reference	1.02291	0.713
57DAP/reference	1.07809	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95611	0.526
17DAP/reference	1.10457	0.405
27DAP/reference	1.1415	0.373
39DAP/reference	1.13943	0.024
41DAP/reference	1.19101	0.08
42DAP/reference	1.26713	0.065
43DAP/reference	1.08113	0.381
47DAP/reference	1.00142	0.731
52DAP/reference	0.99309	0.781
57DAP/reference	1.38062	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96294	1
26DAP/20DAP	0.76516	1
34DAP/26DAP	1.01575	1
51DAP/34DAP	9.0251	0.033
52DAP/51DAP	0.79363	1
53DAP/52DAP	24.355	0.016
55DAP/53DAP	2.04775	0.036
57DAP/55DAP	1.20631	0.34
62DAP/57DAP	1.00003	0.28
68DAP/62DAP	1.25562	0.864
68DAP/14DAP	4.32695	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15202	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.08903	0.046
Mature Green Tomato/Ripe Tomato	0.75153
Immature Eggplant/Mature Eggplant	0.61692	0.134
Ripe Pepper/Ripe Tomato	64.9158	0.239
Mature Eggplant/Ripe Tomato	2.2838	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06477	1
1-1-2/M82	0.90493	1
12-2/M82	1.10385	1
12-4/M82	1.27253	0.438
1-3/M82	0.71625	0.33
2-1-1/M82	1.37185
2-1/M82	N/A	N/A
2-6/M82	0.98764	1
3-2/M82	0.81223
4-1-1/M82	0.94099	1
4-1/M82	1.96776
4-3-2/M82	0.74613
4-3/M82	1.29053	1
5-3/M82	0.937	1
6-2/M82	0.73933	1
6-3/M82	1.00299	1
7-1/M82	0.89834
7-2/M82	0.81439	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.8173	0.247
IL2-6/WTpooled	1.129	0.659
IL7-5/WTpooled	1.30474	1
IL7-3/WTpooled	0.6982	0.418
IL12-4/WTpooled	0.88941	0.581
IL1-4/WTpooled	0.91145	0.699
WT/WTpooled	0.96604	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	2.9701	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06153	0.921
DC3000/delta hrp 6h	1.6421	0.582
DC3000/delta hrp 12h	1.34263	1
DC3000/delta hrp 24h	0.85806	0.662

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	0.85937

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12152	1
Exp 36h	1.15368	0.693
Exp 60h	0.87123	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01484	1
Var 0h	1.74657	0.339
Var 12h I row2-row1	0.74044	0.338
Var 12h NI row2-row1	1.36151	0.34
Var 36h I row2-row1	1.4157	0.489
Var 36h NI row2-row1	0.79402	0.61
Var 60h I row2-row1	0.81988	0.952
Var 60h NI row2-row1	0.82073	0.408
Time course 0hI-0hNI	1.26539	0.163
Time course 12hI-12hNI	0.99172	0.978
Time course 36hI-36hNI	1.29549	0.19
Time course 60hI-60hNI	0.65369	0.009

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)	0.8848	0.409
transgenic ySAMdc/azygous control (breaker)	0.59332	0.173
transgenic ySAMdc/azygous control (red)	1.13378	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86354	0.168

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.38593	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99936	1
Manapal/WT (break)	0.84176	1
Manapal/WT (red)	0.93206	0.728