Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.18.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77136	0.173
27DAP/17DAP	0.92813	0.898
39DAP/27DAP	0.95621	0.682
41DAP/39DAP	1.49919	0.067
42DAP/41DAP	0.95536	1
43DAP/42DAP	0.89708	0.841
47DAP/43DAP	1.14944	0.584
52DAP/47DAP	1.28388	0.608
57DAP/52DAP	1.3369	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9429	0.188
17DAP/reference	1.02723	0.717
27DAP/reference	0.97546	0.694
39DAP/reference	1.05131	0.628
41DAP/reference	0.88143	0.114
42DAP/reference	0.9447	0.151
43DAP/reference	1.0075	0.957
47DAP/reference	0.94359	0.127
52DAP/reference	0.94415	0.215
57DAP/reference	1.05315	0.433

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89505	0.336
27DAP/17DAP	1.00216	0.943
39DAP/27DAP	1.2654	0.429
41DAP/39DAP	0.9211	0.839
42DAP/41DAP	1.12157	0.495
43DAP/42DAP	0.75634	0.037
47DAP/43DAP	1.14359	0.951
52DAP/47DAP	1.21113	0.412
57DAP/52DAP	1.00556	1
57DAP/7DAP	0.72925	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56965	0.047
17DAP/reference	1.86469	0.006
27DAP/reference	1.34661	0.026
39DAP/reference	1.89527	0.006
41DAP/reference	2.04199	0.014
42DAP/reference	2.08755	0.006
43DAP/reference	2.14479	0.006
47DAP/reference	1.40382	0.205
52DAP/reference	1.81338	0.007
57DAP/reference	1.83992	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96883	0.607
17DAP/reference	0.923	0.149
27DAP/reference	0.946	0.269
39DAP/reference	0.91419	0.227
41DAP/reference	0.91429	0.059
42DAP/reference	0.73636	0.012
43DAP/reference	0.87712	0.175
47DAP/reference	0.73883	0.043
52DAP/reference	1.01689	0.882
57DAP/reference	1.03049	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51987	0.017
17DAP/reference	1.2307	0.518
27DAP/reference	1.60067	0.032
39DAP/reference	1.67159	0.016
41DAP/reference	1.59369	0.019
42DAP/reference	1.36834	0.032
43DAP/reference	1.13444	0.565
47DAP/reference	0.90354	0.183
52DAP/reference	1.61115	0.148
57DAP/reference	1.01023	0.661

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03947	1
26DAP/20DAP	1.75352	0.256
34DAP/26DAP	1.23509	0.819
51DAP/34DAP	1.06267	0.795
52DAP/51DAP	1.35761	0.606
53DAP/52DAP	0.80643	0.316
55DAP/53DAP	0.95595	0.784
57DAP/55DAP	1.08208	0.875
62DAP/57DAP	1.09671	1
68DAP/62DAP	1.28876	0.431
68DAP/14DAP	1.33995	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.08596	0.077

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75752	0.257
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.47313
Ripe Pepper/Ripe Tomato	1.71998	0.256
Mature Eggplant/Ripe Tomato	0.78734	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97192	1
12-2/M82	N/A	N/A
12-4/M82	2.17472	1
1-3/M82	N/A	N/A
2-1-1/M82	0.9619	0.465
2-1/M82	0.73071	0.519
2-6/M82	1.16398	0.594
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.97527
4-3-2/M82	N/A	N/A
4-3/M82	1.30162	1
5-3/M82	1.18544	0.378
6-2/M82	N/A	N/A
6-3/M82	1.1172	1
7-1/M82	0.88683	0.443
7-2/M82	1.46754	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91818	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.34644	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	1.01552	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.25092	0.921
DC3000/delta hrp 6h	2.03574	1
DC3000/delta hrp 12h	1.14832	1
DC3000/delta hrp 24h	1.00648	1

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	1.57561

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1695	1
Exp 36h	1.99793	0.371
Exp 60h	2.16378	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04212	1
Var 0h	0.57462	1
Var 12h I row2-row1	1.15753	0.613
Var 12h NI row2-row1	1.22808	0.235
Var 36h I row2-row1	1.31544	0.305
Var 36h NI row2-row1	0.85623	0.706
Var 60h I row2-row1	0.70752	0.374
Var 60h NI row2-row1	1.19792	1
Time course 0hI-0hNI	0.88872	0.185
Time course 12hI-12hNI	0.94901	0.698
Time course 36hI-36hNI	1.30755	0.019
Time course 60hI-60hNI	5.43119	0.008

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)	1.11394	0.292
transgenic ySAMdc/azygous control (breaker)	0.93965	0.49
transgenic ySAMdc/azygous control (red)	1.05283	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04769	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05092	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83425	1
Manapal/WT (break)	0.67637	0.333
Manapal/WT (red)	0.81162	0.181