Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.9.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17279	0.904
27DAP/17DAP	1.12517	0.866
39DAP/27DAP	0.86285	0.594
41DAP/39DAP	1.00579	0.976
42DAP/41DAP	1.02807	1
43DAP/42DAP	1.15277	0.91
47DAP/43DAP	1.11545	0.825
52DAP/47DAP	0.80806	0.565
57DAP/52DAP	1.13821	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7095	0.121
17DAP/reference	0.68628	0.065
27DAP/reference	1.18889	0.264
39DAP/reference	1.00081	1
41DAP/reference	0.91226	0.434
42DAP/reference	0.974	0.359
43DAP/reference	0.84501	0.043
47DAP/reference	0.92378	0.106
52DAP/reference	1.01888	0.749
57DAP/reference	1.23635	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88512	0.388
27DAP/17DAP	1.17792	0.37
39DAP/27DAP	1.08321	0.514
41DAP/39DAP	0.84335	0.465
42DAP/41DAP	0.87595	0.092
43DAP/42DAP	1.07189	0.478
47DAP/43DAP	1.29119	0.63
52DAP/47DAP	1.09907	0.71
57DAP/52DAP	1.29281	0.158
57DAP/7DAP	0.86856	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32317	0.041
17DAP/reference	1.49015	0.017
27DAP/reference	1.36639	0.009
39DAP/reference	1.30284	0.069
41DAP/reference	1.13555	0.314
42DAP/reference	1.05227	1
43DAP/reference	1.31883	0.009
47DAP/reference	1.22362	0.205
52DAP/reference	1.14769	0.563
57DAP/reference	1.31908	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82395	0.076
17DAP/reference	0.782	0.014
27DAP/reference	1.24911	0.526
39DAP/reference	0.97428	0.469
41DAP/reference	1.08868	1
42DAP/reference	0.85695	0.046
43DAP/reference	0.92241	0.352
47DAP/reference	0.81555	0.027
52DAP/reference	0.84997	0.027
57DAP/reference	0.74825	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22104	0.149
17DAP/reference	1.04152	1
27DAP/reference	1.52364	0.023
39DAP/reference	1.37853	0.01
41DAP/reference	1.07552	0.657
42DAP/reference	1.24393	0.082
43DAP/reference	1.38291	0.087
47DAP/reference	0.89718	0.066
52DAP/reference	1.58265	0.082
57DAP/reference	1.32381	0.055

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93661	1
26DAP/20DAP	0.83552	1
34DAP/26DAP	0.97323	0.98
51DAP/34DAP	0.99927	0.927
52DAP/51DAP	1.0785	1
53DAP/52DAP	1.23369	0.858
55DAP/53DAP	1.95215	0.861
57DAP/55DAP	1.19717	0.955
62DAP/57DAP	1.14875	0.767
68DAP/62DAP	1.7471	0.31
68DAP/14DAP	1.29712	0.17

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.46085	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.72658	0.331
Immature Eggplant/Mature Eggplant	0.49369
Ripe Pepper/Ripe Tomato	0.19915	1
Mature Eggplant/Ripe Tomato	0.60398	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12995	0.877
1-1-2/M82	1.28726
12-2/M82	0.84096	0.721
12-4/M82	1.21955	1
1-3/M82	1.22211
2-1-1/M82	1.02591	0.764
2-1/M82	0.79766
2-6/M82	0.92125	1
3-2/M82	1.06954	0.967
4-1-1/M82	1.066	1
4-1/M82	N/A	N/A
4-3-2/M82	0.96741	1
4-3/M82	1.09093	1
5-3/M82	1.18261	1
6-2/M82	1.35601	1
6-3/M82	0.88281	0.619
7-1/M82	N/A	N/A
7-2/M82	1.24807	0.282
9-3-2/M82	1.1661	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.23704	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00234	1
IL12-4/WTpooled	1.13813	0.52
IL1-4/WTpooled	0.96254
WT/WTpooled	1.03453	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	1.10299	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01471	1
DC3000/delta hrp 6h	1.05517	0.95
DC3000/delta hrp 12h	1.09986	1
DC3000/delta hrp 24h	0.8543	0.178

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.03797	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07862	1
Exp 36h	0.92818	0.82
Exp 60h	1.01444	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99195	1
Var 0h	0.93032	1
Var 12h I row2-row1	0.95303	0.357
Var 12h NI row2-row1	1.08835	1
Var 36h I row2-row1	0.92333	1
Var 36h NI row2-row1	1.00999	1
Var 60h I row2-row1	0.91453	0.832
Var 60h NI row2-row1	0.9273	0.69
Time course 0hI-0hNI	1.02661	0.852
Time course 12hI-12hNI	0.87296	0.089
Time course 36hI-36hNI	0.87482	0.033
Time course 60hI-60hNI	0.88507	0.161

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)	1.11766	0.25
transgenic ySAMdc/azygous control (breaker)	1.07107	1
transgenic ySAMdc/azygous control (red)	1.04747	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96497	0.133

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98968	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73593	0.172
Manapal/WT (break)	0.8253	0.333
Manapal/WT (red)	1.04035	1