Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.924	0.503
27DAP/17DAP	0.99247	1
39DAP/27DAP	1.09849	0.853
41DAP/39DAP	0.87887	0.518
42DAP/41DAP	1.04923	0.994
43DAP/42DAP	0.8689	0.643
47DAP/43DAP	1.16402	0.455
52DAP/47DAP	1.11412	0.837
57DAP/52DAP	0.99982	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26645	0.022
17DAP/reference	0.95857	0.419
27DAP/reference	0.89946	0.163
39DAP/reference	0.95261	0.381
41DAP/reference	0.97277	0.667
42DAP/reference	1.15828	0.001
43DAP/reference	0.99372	0.84
47DAP/reference	1.18253	0.032
52DAP/reference	1.08863	0.217
57DAP/reference	1.06803	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98593	0.763
27DAP/17DAP	0.81776	0.172
39DAP/27DAP	0.99245	1
41DAP/39DAP	1.13837	0.439
42DAP/41DAP	0.90971	0.298
43DAP/42DAP	0.94869	0.466
47DAP/43DAP	0.96302	0.774
52DAP/47DAP	1.19876	0.478
57DAP/52DAP	1.22938	0.197
57DAP/7DAP	0.91631	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21149	0.227
17DAP/reference	1.4896	0.007
27DAP/reference	1.37354	0.006
39DAP/reference	1.06051	0.333
41DAP/reference	1.20477	0.026
42DAP/reference	1.29853	0.007
43DAP/reference	1.19227	0.021
47DAP/reference	1.20198	0.104
52DAP/reference	1.47214	0.007
57DAP/reference	1.35461	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08501	0.443
17DAP/reference	1.1825	0.065
27DAP/reference	1.35465	0.063
39DAP/reference	1.20626	0.29
41DAP/reference	1.38324	0.02
42DAP/reference	1.39615	0.009
43DAP/reference	1.12248	0.526
47DAP/reference	1.32557	0.051
52DAP/reference	1.22267	0.156
57DAP/reference	1.13091	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32507	0.019
17DAP/reference	1.22817	0.194
27DAP/reference	0.98946	0.657
39DAP/reference	1.22358	0.011
41DAP/reference	1.17406	0.028
42DAP/reference	1.30182	0.039
43DAP/reference	1.16996	0.474
47DAP/reference	1.03092	0.704
52DAP/reference	1.38137	0.067
57DAP/reference	1.61388	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04498	1
26DAP/20DAP	0.98019	1
34DAP/26DAP	1.38257	0.819
51DAP/34DAP	0.816	0.369
52DAP/51DAP	1.7565	0.036
53DAP/52DAP	0.7193	0.051
55DAP/53DAP	1.341	0.066
57DAP/55DAP	0.76683	0.294
62DAP/57DAP	1.01145	0.902
68DAP/62DAP	0.96618	0.834
68DAP/14DAP	1.23413	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94823	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.24355	0.058
Mature Green Tomato/Ripe Tomato	1.31239	0.632
Immature Eggplant/Mature Eggplant	1.08925	0.398
Ripe Pepper/Ripe Tomato	0.8621	1
Mature Eggplant/Ripe Tomato	0.91909	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09569	0.742
1-1-2/M82	0.994	1
12-2/M82	1.18207	1
12-4/M82	0.99176	1
1-3/M82	0.9842	1
2-1-1/M82	1.19268
2-1/M82	0.82285	0.519
2-6/M82	0.97842	1
3-2/M82	0.82307
4-1-1/M82	1.02512	1
4-1/M82	0.98164
4-3-2/M82	1.02241
4-3/M82	1.31502	1
5-3/M82	1.17539	1
6-2/M82	0.85367
6-3/M82	0.94219	1
7-1/M82	0.77285
7-2/M82	0.91883	0.796
9-3-2/M82	0.90694

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
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	N/A	N/A
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	1.01514	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16289	0.875
DC3000/delta hrp 6h	0.95586	0.95
DC3000/delta hrp 12h	1.06676	1
DC3000/delta hrp 24h	1.08268	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35053	0.16
DC3000 delta B/DC3000 delta AB	1.15396	0.327

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	0.94773	1
Var 0h	0.4258	0.933
Var 12h I row2-row1	0.90671	0.39
Var 12h NI row2-row1	0.92941	0.906
Var 36h I row2-row1	0.86267	1
Var 36h NI row2-row1	1.16638	1
Var 60h I row2-row1	1.17371	0.523
Var 60h NI row2-row1	0.93927	1
Time course 0hI-0hNI	0.90071	0.23
Time course 12hI-12hNI	1.0557	0.517
Time course 36hI-36hNI	1.09362	0.651
Time course 60hI-60hNI	1.21639	0.16

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)	0.9172	0.391
transgenic ySAMdc/azygous control (breaker)	1.74902	0.166
transgenic ySAMdc/azygous control (red)	1.05572	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06239	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68312	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75969	0.172
Manapal/WT (break)	0.91735	0.299
Manapal/WT (red)	1.77613	0.134