Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.1.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94092	0.558
27DAP/17DAP	0.6603	0.048
39DAP/27DAP	0.81313	0.447
41DAP/39DAP	0.60571	0.045
42DAP/41DAP	0.86227	1
43DAP/42DAP	1.45076	0.279
47DAP/43DAP	0.6489	0.132
52DAP/47DAP	0.62577	0.131
57DAP/52DAP	0.80053	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43738	0.126
17DAP/reference	1.07207	0.874
27DAP/reference	1.30972	0.044
39DAP/reference	1.02125	0.975
41DAP/reference	1.44197	0.265
42DAP/reference	1.19482	0.252
43DAP/reference	1.21757	0.547
47DAP/reference	1.14241	0.478
52DAP/reference	0.96486	0.489
57DAP/reference	0.96719	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94504	0.595
27DAP/17DAP	0.88112	0.648
39DAP/27DAP	0.56874	0.041
41DAP/39DAP	0.99632	0.98
42DAP/41DAP	0.85957	0.387
43DAP/42DAP	0.57951	0.022
47DAP/43DAP	1.03436	0.997
52DAP/47DAP	0.92986	0.739
57DAP/52DAP	0.98635	0.737
57DAP/7DAP	0.66987	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.00325	0.024
17DAP/reference	1.48045	0.064
27DAP/reference	1.03585	0.664
39DAP/reference	1.09645	0.282
41DAP/reference	0.73367	0.04
42DAP/reference	1.23033	0.686
43DAP/reference	0.95624	0.279
47DAP/reference	1.0467	1
52DAP/reference	0.95924	0.398
57DAP/reference	1.03943	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84614	0.277
17DAP/reference	1.02515	0.898
27DAP/reference	1.22973	0.822
39DAP/reference	1.50728	0.013
41DAP/reference	1.2425	0.737
42DAP/reference	1.28873	0.039
43DAP/reference	0.89323	0.307
47DAP/reference	1.12773	0.098
52DAP/reference	0.60084	0.171
57DAP/reference	1.07498	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86604	0.02
17DAP/reference	1.64862	0.15
27DAP/reference	1.41606	0.051
39DAP/reference	1.07202	0.13
41DAP/reference	0.936	0.56
42DAP/reference	1.17101	0.45
43DAP/reference	0.92966	0.398
47DAP/reference	1.05726	0.901
52DAP/reference	0.75327	0.277
57DAP/reference	1.24042	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10927
26DAP/20DAP	1.11662	0.813
34DAP/26DAP	0.94258	0.861
51DAP/34DAP	0.87702	0.323
52DAP/51DAP	0.9727	1
53DAP/52DAP	1.02122	1
55DAP/53DAP	0.56728	0.016
57DAP/55DAP	1.2828	0.865
62DAP/57DAP	1.04657	1
68DAP/62DAP	0.47679
68DAP/14DAP	1.51252

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.25379	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	5.46955	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	7.50165
Mature Eggplant/Ripe Tomato	9.52436	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.92031	0.473
1-1-2/M82	1.11517	1
12-2/M82	0.56937	0.678
12-4/M82	0.72707	0.619
1-3/M82	1.18054
2-1-1/M82	1.23513	1
2-1/M82	0.68002	0.322
2-6/M82	4.42289	0.329
3-2/M82	0.84244
4-1-1/M82	0.58867
4-1/M82	N/A	N/A
4-3-2/M82	2.34418
4-3/M82	1.42262	1
5-3/M82	0.77987	1
6-2/M82	2.11887	0.195
6-3/M82	N/A	N/A
7-1/M82	0.67053
7-2/M82	1.80198	0.291
9-3-2/M82	2.24359	0.171

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0021	1
IL2-6/WTpooled	1.01179	1
IL7-5/WTpooled	0.86059	1
IL7-3/WTpooled	0.94121	1
IL12-4/WTpooled	0.64746	0.566
IL1-4/WTpooled	0.9597	0.834
WT/WTpooled	1.03724	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	1.05064	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95962	1
DC3000/delta hrp 6h	1.22676	1
DC3000/delta hrp 12h	1.31207	1
DC3000/delta hrp 24h	0.62035	0.06

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.479
DC3000 delta B/DC3000 delta AB	0.53337	0.021

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.086	1
Var 0h	0.48325	1
Var 12h I row2-row1	0.79045	0.338
Var 12h NI row2-row1	0.97291	0.906
Var 36h I row2-row1	0.86961	0.805
Var 36h NI row2-row1	1.42163	1
Var 60h I row2-row1	1.10287	1
Var 60h NI row2-row1	1.06669	1
Time course 0hI-0hNI	0.9874	0.991
Time course 12hI-12hNI	1.01744	1
Time course 36hI-36hNI	0.88773	0.052
Time course 60hI-60hNI	0.12831	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.9704	1
transgenic ySAMdc/azygous control (red)	1.29662	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.18555	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18524	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.10937	0.083
Manapal/WT (break)	1.31708	0.123
Manapal/WT (red)	3.51606	0.133