Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22789	0.523
27DAP/17DAP	0.55843	0.049
39DAP/27DAP	0.84229	0.529
41DAP/39DAP	0.58259	0.045
42DAP/41DAP	1.09981	0.899
43DAP/42DAP	1.13593	0.993
47DAP/43DAP	0.90155	0.667
52DAP/47DAP	1.13792	0.903
57DAP/52DAP	1.17066	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7144	0.025
17DAP/reference	0.51828	0.007
27DAP/reference	0.51076	0.016
39DAP/reference	0.34501	0.009
41DAP/reference	1.02903	0.814
42DAP/reference	0.60462	0.014
43DAP/reference	0.29811
47DAP/reference	0.63439	0.014
52DAP/reference	0.34652	0.014
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60542	0.05
27DAP/17DAP	0.71055	0.218
39DAP/27DAP	0.64053	0.064
41DAP/39DAP	1.16229	0.258
42DAP/41DAP	0.79113	0.033
43DAP/42DAP	0.79865	0.041
47DAP/43DAP	0.85131	0.16
52DAP/47DAP	0.99761	0.959
57DAP/52DAP	0.86297	0.349
57DAP/7DAP	0.58195	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17187	0.197
17DAP/reference	1.06061	0.971
27DAP/reference	0.83783	0.055
39DAP/reference	1.08199	0.634
41DAP/reference	0.91515	0.284
42DAP/reference	1.19602	0.233
43DAP/reference	1.17783	0.079
47DAP/reference	0.64988	0.128
52DAP/reference	0.98558	0.571
57DAP/reference	1.0009	0.61

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56723	0.051
17DAP/reference	0.47582	0.021
27DAP/reference	0.67019	0.081
39DAP/reference	0.46344	0.012
41DAP/reference	0.66811	0.047
42DAP/reference	0.53933	0.012
43DAP/reference	0.58118	0.017
47DAP/reference	0.55078	0.007
52DAP/reference	0.39889	0.004
57DAP/reference	0.37472	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30484	0.042
17DAP/reference	1.2795	0.224
27DAP/reference	1.07611	0.408
39DAP/reference	1.15764	0.633
41DAP/reference	1.02264	1
42DAP/reference	0.76575	0.172
43DAP/reference	0.67003	0.054
47DAP/reference	0.44746	0.004
52DAP/reference	0.63096	0.131
57DAP/reference	0.6722	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16502	0.966
26DAP/20DAP	0.93032	1
34DAP/26DAP	0.95786	0.917
51DAP/34DAP	0.58963	0.058
52DAP/51DAP	1.08226	0.792
53DAP/52DAP	0.85807	0.27
55DAP/53DAP	1.13389	0.719
57DAP/55DAP	1.14481	0.805
62DAP/57DAP	1.13605	0.622
68DAP/62DAP	0.76893	0.29
68DAP/14DAP	0.58081	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54186	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.45073	0.058
Mature Green Tomato/Ripe Tomato	2.84933	0.015
Immature Eggplant/Mature Eggplant	0.42031	0.062
Ripe Pepper/Ripe Tomato	6.34969	1
Mature Eggplant/Ripe Tomato	4.44868	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00063	1
1-1-2/M82	0.99029	1
12-2/M82	0.62121
12-4/M82	1.06694
1-3/M82	0.97427	1
2-1-1/M82	0.81565
2-1/M82	N/A	N/A
2-6/M82	1.1504	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.03696	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.07319	1
5-3/M82	1.13227	1
6-2/M82	0.85212	1
6-3/M82	1.22351
7-1/M82	N/A	N/A
7-2/M82	1.02409	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.78265	0.247
IL2-6/WTpooled	1.07698	0.659
IL7-5/WTpooled	1.0459	1
IL7-3/WTpooled	0.73276	0.31
IL12-4/WTpooled	1.04788	0.737
IL1-4/WTpooled	0.88166	0.476
WT/WTpooled	0.9513	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	0.98108	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99614	1
DC3000/delta hrp 6h	0.95581	0.95
DC3000/delta hrp 12h	1.20941	1
DC3000/delta hrp 24h	0.84851	0.225

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.60468	0.047
DC3000 delta B/DC3000 delta AB	0.40983	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03332	1
Exp 36h	0.83145	0.661
Exp 60h	0.81233	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.25836	1
Var 0h	2.56214	1
Var 12h I row2-row1	0.61674	0.357
Var 12h NI row2-row1	0.82101	0.546
Var 36h I row2-row1	0.88603	0.805
Var 36h NI row2-row1	1.08376	1
Var 60h I row2-row1	0.7515	0.832
Var 60h NI row2-row1	1.01125	1
Time course 0hI-0hNI	0.97581	0.886
Time course 12hI-12hNI	0.91116	0.144
Time course 36hI-36hNI	0.75802	0.041
Time course 60hI-60hNI	0.1758	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)	1.09546	0.798
transgenic ySAMdc/azygous control (breaker)	2.81823	0.166
transgenic ySAMdc/azygous control (red)	1.04925	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.58442	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.71025	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	15.929	0.084
Manapal/WT (break)	9.63692	0.123
Manapal/WT (red)	1.32837	1