Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.19.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81931	0.226
27DAP/17DAP	1.13773	0.88
39DAP/27DAP	0.88909	0.549
41DAP/39DAP	1.29175	0.392
42DAP/41DAP	1.0657	1
43DAP/42DAP	1.00137	0.937
47DAP/43DAP	1.23936	0.538
52DAP/47DAP	1.05867	0.953
57DAP/52DAP	1.01592	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89976	0.194
17DAP/reference	0.73467	0.053
27DAP/reference	0.7737	0.208
39DAP/reference	0.97636	0.797
41DAP/reference	0.66738	0.026
42DAP/reference	0.86268	0.04
43DAP/reference	0.71199
47DAP/reference	0.84052	0.083
52DAP/reference	0.96951	0.36
57DAP/reference	1.12635

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16223	0.662
27DAP/17DAP	1.02289	0.957
39DAP/27DAP	0.99715	1
41DAP/39DAP	1.33951	0.112
42DAP/41DAP	0.86426	0.245
43DAP/42DAP	0.98344	0.854
47DAP/43DAP	1.05506	0.678
52DAP/47DAP	0.93339	0.777
57DAP/52DAP	1.26286	0.106
57DAP/7DAP	1.0925	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97289	0.495
17DAP/reference	0.89167	0.072
27DAP/reference	0.97544	0.43
39DAP/reference	1.18365	0.069
41DAP/reference	0.92647	0.298
42DAP/reference	1.02492	0.889
43DAP/reference	1.05768	0.83
47DAP/reference	1.04338	1
52DAP/reference	0.93472	0.196
57DAP/reference	0.81357	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87098	0.152
17DAP/reference	0.9287	0.297
27DAP/reference	0.9643	0.467
39DAP/reference	1.06814	0.868
41DAP/reference	1.07112	0.48
42DAP/reference	0.98334	0.594
43DAP/reference	0.84479	0.157
47DAP/reference	0.85439	0.049
52DAP/reference	1.07489	0.498
57DAP/reference	0.82052	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92131	0.119
17DAP/reference	0.94301	0.398
27DAP/reference	0.9493	0.184
39DAP/reference	0.98328	0.643
41DAP/reference	0.99423	0.682
42DAP/reference	1.16331	0.272
43DAP/reference	1.21332	0.349
47DAP/reference	1.02165	1
52DAP/reference	1.10187	0.735
57DAP/reference	1.55217	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25	0.966
26DAP/20DAP	0.89204	1
34DAP/26DAP	1.43435	0.819
51DAP/34DAP	0.92622	0.698
52DAP/51DAP	1.00975	0.965
53DAP/52DAP	1.0964	0.91
55DAP/53DAP	1.18637	0.599
57DAP/55DAP	0.98936	0.888
62DAP/57DAP	1.15654	0.393
68DAP/62DAP	1.74846	0.153
68DAP/14DAP	2.8017	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35523	0.162

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.45837	0.063
Mature Green Tomato/Ripe Tomato	1.19393	1
Immature Eggplant/Mature Eggplant	0.5662	0.063
Ripe Pepper/Ripe Tomato	0.68582	1
Mature Eggplant/Ripe Tomato	0.9421	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06784	0.536
1-1-2/M82	1.10435	1
12-2/M82	1.01001	1
12-4/M82	1.10807	1
1-3/M82	1.39463	0.248
2-1-1/M82	0.93299	0.683
2-1/M82	0.64522	0.322
2-6/M82	0.98912	1
3-2/M82	1.24927
4-1-1/M82	1.00037	1
4-1/M82	1.00949
4-3-2/M82	1.14955
4-3/M82	1.32291	1
5-3/M82	1.12483	1
6-2/M82	0.93828	1
6-3/M82	0.98273	1
7-1/M82	0.97427	0.803
7-2/M82	1.09632	0.299
9-3-2/M82	1.1102	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94212	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.86902	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.98333	1
WT/WTpooled	N/A	N/A

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	0.90766	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03606	0.921
DC3000/delta hrp 6h	0.95797	0.95
DC3000/delta hrp 12h	1.0077	1
DC3000/delta hrp 24h	0.96284	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79339	0.293
DC3000 delta B/DC3000 delta AB	0.81993	0.21

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93587	1
Exp 36h	0.68181	0.374
Exp 60h	0.71161	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06133	1
Var 0h	0.98164	1
Var 12h I row2-row1	0.99099	1
Var 12h NI row2-row1	1.01351	1
Var 36h I row2-row1	1.01753	1
Var 36h NI row2-row1	0.89367	0.645
Var 60h I row2-row1	0.83928	0.582
Var 60h NI row2-row1	0.94719	0.818
Time course 0hI-0hNI	1.09001	0.764
Time course 12hI-12hNI	0.93872	0.497
Time course 36hI-36hNI	0.93102	0.134
Time course 60hI-60hNI	0.86161	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)	1.1172	0.326
transgenic ySAMdc/azygous control (breaker)	1.00603	1
transgenic ySAMdc/azygous control (red)	1.06614	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87664	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.7913	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96128	1
Manapal/WT (break)	1.25017	0.123
Manapal/WT (red)	1.06969	1