Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.12.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58623	0.043
27DAP/17DAP	1.30476	0.735
39DAP/27DAP	2.88528	0.02
41DAP/39DAP	0.84016	0.409
42DAP/41DAP	1.98683	0.037
43DAP/42DAP	0.82433	0.589
47DAP/43DAP	0.84305	0.517
52DAP/47DAP	1.14642	0.851
57DAP/52DAP	0.97888	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73168	0.027
17DAP/reference	0.79414	0.019
27DAP/reference	0.81387	0.037
39DAP/reference	0.7884	0.074
41DAP/reference	0.75663	0.039
42DAP/reference	0.77255	0.001
43DAP/reference	0.78498	0.021
47DAP/reference	0.76684	0.001
52DAP/reference	0.79548	0.053
57DAP/reference	0.89568	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.4302	0.036
27DAP/17DAP	0.3932	0.079
39DAP/27DAP	1.5687	0.09
41DAP/39DAP	1.02108	1
42DAP/41DAP	1.51457	0.007
43DAP/42DAP	0.5828	0.025
47DAP/43DAP	1.26455	0.024
52DAP/47DAP	0.64201	0.136
57DAP/52DAP	0.84145	0.476
57DAP/7DAP	1.45155	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19796	0.241
17DAP/reference	1.38382	0.059
27DAP/reference	1.16061	0.088
39DAP/reference	1.07982	0.57
41DAP/reference	1.07881	0.56
42DAP/reference	1.05324	0.889
43DAP/reference	1.06314	0.537
47DAP/reference	0.97901	0.671
52DAP/reference	0.96481	0.304
57DAP/reference	1.12713	0.108

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70676	0.007
17DAP/reference	0.71411	0.005
27DAP/reference	0.7613	0.021
39DAP/reference	0.7723	0.039
41DAP/reference	0.76498	0.011
42DAP/reference	0.76243	0.015
43DAP/reference	0.9755	0.607
47DAP/reference	0.81824	0.026
52DAP/reference	0.65701	0.004
57DAP/reference	0.83121	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04112	0.984
17DAP/reference	0.93127	0.444
27DAP/reference	1.20642	0.164
39DAP/reference	1.20091	0.134
41DAP/reference	1.09176	0.369
42DAP/reference	0.91867	0.22
43DAP/reference	0.86351	0.206
47DAP/reference	0.74045	0.01
52DAP/reference	1.73461	0.179
57DAP/reference	1.0421	0.5

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.37325	0.966
26DAP/20DAP	0.91837	1
34DAP/26DAP	1.78759	0.106
51DAP/34DAP	7.65928	0.021
52DAP/51DAP	0.69782	0.151
53DAP/52DAP	1.34756	0.044
55DAP/53DAP	0.52824	0.016
57DAP/55DAP	0.7159	0.093
62DAP/57DAP	0.8872	0.681
68DAP/62DAP	0.94078	0.747
68DAP/14DAP	3.06878	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.06469	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.15325	0.051
Mature Green Tomato/Ripe Tomato	1.25234	0.632
Immature Eggplant/Mature Eggplant	6.57546	0.05
Ripe Pepper/Ripe Tomato	19.2826	0.256
Mature Eggplant/Ripe Tomato	8.19195	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.82346
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.22203
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.75634
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.0427

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81816	0.321
IL2-6/WTpooled	0.9475	0.473
IL7-5/WTpooled	4.44437	0.792
IL7-3/WTpooled	1.03296	1
IL12-4/WTpooled	0.91942	0.71
IL1-4/WTpooled	1.63976	0.426
WT/WTpooled	0.99284	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	2.30293	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05641	0.846
DC3000/delta hrp 6h	1.19509	1
DC3000/delta hrp 12h	1.18857	1
DC3000/delta hrp 24h	0.76084	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17002	0.27
DC3000 delta B/DC3000 delta AB	1.74907	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.26183	1
Exp 36h	1.08494	0.693
Exp 60h	1.65727	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0594	1
Var 0h	0.52709	0.782
Var 12h I row2-row1	1.44249	0.443
Var 12h NI row2-row1	1.55562	0.281
Var 36h I row2-row1	1.59555	0.489
Var 36h NI row2-row1	0.93392	0.706
Var 60h I row2-row1	0.60917	0.285
Var 60h NI row2-row1	1.04014	1
Time course 0hI-0hNI	1.08051	0.719
Time course 12hI-12hNI	0.95684	0.776
Time course 36hI-36hNI	1.20897	0.035
Time course 60hI-60hNI	5.85802	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)	1.23088	0.612
transgenic ySAMdc/azygous control (breaker)	0.97693	1
transgenic ySAMdc/azygous control (red)	0.96003	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.95689	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08128	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.5839	0.088
Manapal/WT (break)	1.00064	1
Manapal/WT (red)	0.80517	0.242