Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78098	0.169
27DAP/17DAP	0.65775	0.138
39DAP/27DAP	0.81488	0.474
41DAP/39DAP	0.62799	0.068
42DAP/41DAP	1.00371	1
43DAP/42DAP	1.03314	1
47DAP/43DAP	1.0041	0.972
52DAP/47DAP	1.4415	0.449
57DAP/52DAP	0.99235	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09828	0.188
17DAP/reference	0.9839	0.737
27DAP/reference	0.98689	0.694
39DAP/reference	0.88106	0.068
41DAP/reference	0.84207	0.039
42DAP/reference	0.94106	0.034
43DAP/reference	0.92866	0.259
47DAP/reference	0.93237	0.05
52DAP/reference	0.85917	0.111
57DAP/reference	1.03665	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80553	0.078
27DAP/17DAP	1.04616	0.788
39DAP/27DAP	0.82874	0.11
41DAP/39DAP	0.8768	0.112
42DAP/41DAP	1.00321	1
43DAP/42DAP	0.96705	0.618
47DAP/43DAP	0.99172	0.961
52DAP/47DAP	1.01628	0.956
57DAP/52DAP	0.95236	0.581
57DAP/7DAP	0.55218	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59284	0.024
17DAP/reference	0.89573	0.015
27DAP/reference	0.61479	0.01
39DAP/reference	0.58985	0.011
41DAP/reference	0.49105	0.011
42DAP/reference	0.50982	0.011
43DAP/reference	0.38228	0.01
47DAP/reference	0.70754	0.168
52DAP/reference	0.41219	0.009
57DAP/reference	0.45709	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04968	0.758
17DAP/reference	1.03913	0.69
27DAP/reference	0.94133	0.249
39DAP/reference	0.77179	0.013
41DAP/reference	0.85367	0.052
42DAP/reference	0.87424	0.011
43DAP/reference	0.72782	0.054
47DAP/reference	0.9312	0.049
52DAP/reference	0.78993	0.004
57DAP/reference	0.79907	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.2911	0.017
17DAP/reference	1.50152	0.111
27DAP/reference	1.10467	0.096
39DAP/reference	0.9872	0.643
41DAP/reference	0.80636	0.055
42DAP/reference	0.68549	0.028
43DAP/reference	0.70572	0.024
47DAP/reference	0.7977	0.016
52DAP/reference	0.53704	0.059
57DAP/reference	1.08871	0.428

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10152	0.966
26DAP/20DAP	0.93467	0.512
34DAP/26DAP	1.00162	1
51DAP/34DAP	0.71077	0.06
52DAP/51DAP	1.07753	0.42
53DAP/52DAP	0.92887	0.52
55DAP/53DAP	0.9655	0.663
57DAP/55DAP	0.94779	0.78
62DAP/57DAP	1.03829	0.622
68DAP/62DAP	0.58296	0.032
68DAP/14DAP	0.9311	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78401	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.18433	0.058
Mature Green Tomato/Ripe Tomato	6.76263	0.015
Immature Eggplant/Mature Eggplant	0.49324	0.063
Ripe Pepper/Ripe Tomato	1.88193	1
Mature Eggplant/Ripe Tomato	9.00567	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94543	0.944
1-1-2/M82	0.68903
12-2/M82	N/A	N/A
12-4/M82	1.07258	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.60722
2-6/M82	1.23417	0.505
3-2/M82	1.31015
4-1-1/M82	0.90571	1
4-1/M82	0.85987
4-3-2/M82	1.30962
4-3/M82	1.23012
5-3/M82	1.10316	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.08374
7-2/M82	0.95267
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88671
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.22643	1
IL12-4/WTpooled	1.08457	0.737
IL1-4/WTpooled	0.93376	1
WT/WTpooled	0.9382

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	0.94582	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94625	1
DC3000/delta hrp 6h	1.13517	1
DC3000/delta hrp 12h	0.92173	1
DC3000/delta hrp 24h	0.84643	0.159

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46181	0.024
DC3000 delta B/DC3000 delta AB	0.47826	0.02

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	0.99291	1
Var 0h	1.14414	0.594
Var 12h I row2-row1	0.81494	0.353
Var 12h NI row2-row1	0.94776	0.627
Var 36h I row2-row1	0.84343	0.805
Var 36h NI row2-row1	0.97868	0.791
Var 60h I row2-row1	1.24334	0.523
Var 60h NI row2-row1	1.01506	1
Time course 0hI-0hNI	1.0114	1
Time course 12hI-12hNI	0.98331	0.906
Time course 36hI-36hNI	0.91237	0.062
Time course 60hI-60hNI	0.2928	0.006

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)	1.05459	0.511
transgenic ySAMdc/azygous control (breaker)	2.26287	0.178
transgenic ySAMdc/azygous control (red)	0.95751	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.83428	0.067

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.75558	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.54255	0.084
Manapal/WT (break)	5.25434	0.123
Manapal/WT (red)	1.63606	0.222