Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0597	0.878
27DAP/17DAP	1.16887	0.833
39DAP/27DAP	0.8831	0.522
41DAP/39DAP	0.95395	0.771
42DAP/41DAP	1.00359	1
43DAP/42DAP	1.067	1
47DAP/43DAP	1.278	0.527
52DAP/47DAP	0.88556	0.675
57DAP/52DAP	0.99861	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14314	0.121
17DAP/reference	1.16286	0.442
27DAP/reference	1.24188	0.025
39DAP/reference	1.12117	0.545
41DAP/reference	1.23032	0.043
42DAP/reference	1.1052	0.585
43DAP/reference	1.01527	1
47DAP/reference	1.11479	0.254
52DAP/reference	1.06114	0.73
57DAP/reference	1.15618	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10235	0.422
27DAP/17DAP	0.85919	0.58
39DAP/27DAP	1.09907	0.394
41DAP/39DAP	0.86302	0.347
42DAP/41DAP	1.14609	0.028
43DAP/42DAP	1.21883	0.324
47DAP/43DAP	0.94721	0.712
52DAP/47DAP	1.1544	0.527
57DAP/52DAP	0.96224	0.584
57DAP/7DAP	1.23142	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80151	0.059
17DAP/reference	0.92505	0.094
27DAP/reference	0.84534	0.019
39DAP/reference	0.91716	0.095
41DAP/reference	1.00316	0.811
42DAP/reference	0.95293	0.2
43DAP/reference	1.07666	0.256
47DAP/reference	1.09399	0.285
52DAP/reference	0.9416	0.163
57DAP/reference	0.92464	0.162

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97139	0.72
17DAP/reference	1.13899	0.674
27DAP/reference	1.16434	0.367
39DAP/reference	1.23351	0.15
41DAP/reference	1.36477	0.02
42DAP/reference	1.34513	0.105
43DAP/reference	1.00188	0.516
47DAP/reference	2.01518	0.008
52DAP/reference	1.40217	0.034
57DAP/reference	1.07888	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74133	0.027
17DAP/reference	0.99693	0.778
27DAP/reference	0.83291	0.036
39DAP/reference	0.98803	0.643
41DAP/reference	0.96598	0.512
42DAP/reference	1.10871	0.51
43DAP/reference	1.19448	0.098
47DAP/reference	1.17383	0.228
52DAP/reference	1.14269	0.759
57DAP/reference	1.12111	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.43407	0.945
26DAP/20DAP	1.1959	0.39
34DAP/26DAP	1.02511	1
51DAP/34DAP	1.94837	0.033
52DAP/51DAP	0.81885	0.151
53DAP/52DAP	1.64516	0.031
55DAP/53DAP	0.84868	0.088
57DAP/55DAP	0.68926	0.057
62DAP/57DAP	1.22262	0.678
68DAP/62DAP	1.00881	0.863
68DAP/14DAP	0.90152	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01447	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.10677	0.046
Mature Green Tomato/Ripe Tomato	0.86753
Immature Eggplant/Mature Eggplant	2.90848	0.05
Ripe Pepper/Ripe Tomato	4.06277	0.256
Mature Eggplant/Ripe Tomato	0.97385	1

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	1.11064	1
1-3/M82	1.59856
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.24048	0.241
4-3/M82	N/A	N/A
5-3/M82	1.23809	0.427
6-2/M82	1.79416
6-3/M82	0.80908	1
7-1/M82	0.93964
7-2/M82	1.3434
9-3-2/M82	1.38901	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97409
IL2-6/WTpooled	0.8712	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05378	1
IL12-4/WTpooled	1.18212	0.538
IL1-4/WTpooled	0.91102	0.834
WT/WTpooled	1.00108	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	0.98043	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93763	1
DC3000/delta hrp 6h	0.84884	0.95
DC3000/delta hrp 12h	1.03107	1
DC3000/delta hrp 24h	0.90809	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.78445	0.022
DC3000 delta B/DC3000 delta AB	2.21808	0.051

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17188	1
Exp 36h	1.3937	1
Exp 60h	1.02245	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03715	1
Var 0h	1.77073	0.936
Var 12h I row2-row1	0.81234	0.338
Var 12h NI row2-row1	0.90377	0.627
Var 36h I row2-row1	1.11475	1
Var 36h NI row2-row1	1.02712	1
Var 60h I row2-row1	1.03336	1
Var 60h NI row2-row1	0.95407	0.818
Time course 0hI-0hNI	1.05673	0.799
Time course 12hI-12hNI	0.99234	1
Time course 36hI-36hNI	0.83199	0.033
Time course 60hI-60hNI	0.72155	0.026

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)	0.93026	0.338
transgenic ySAMdc/azygous control (breaker)	0.66918	0.131
transgenic ySAMdc/azygous control (red)	0.98647	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.33662	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58673	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.72792	0.09
Manapal/WT (break)	1.07018	0.381
Manapal/WT (red)	1.28461	0.164