Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.12.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83028	0.427
27DAP/17DAP	0.97083	0.994
39DAP/27DAP	1.24805	0.74
41DAP/39DAP	0.96894	0.862
42DAP/41DAP	3.38089	0.043
43DAP/42DAP	1.166	0.945
47DAP/43DAP	2.09331	0.156
52DAP/47DAP	0.47212	0.052
57DAP/52DAP	1.31284	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10775	0.188
17DAP/reference	1.01629	0.813
27DAP/reference	1.12652	0.179
39DAP/reference	1.28602	0.015
41DAP/reference	1.13409	0.062
42DAP/reference	1.2457	0.062
43DAP/reference	1.11111	0.095
47DAP/reference	1.10747	0.558
52DAP/reference	0.95803	0.416
57DAP/reference	1.04259	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.40754	0.038
27DAP/17DAP	1.23231	0.447
39DAP/27DAP	1.11138	0.626
41DAP/39DAP	0.65993	0.164
42DAP/41DAP	1.30816	0.139
43DAP/42DAP	3.50608	0.013
47DAP/43DAP	1.31411	0.012
52DAP/47DAP	0.69649	0.121
57DAP/52DAP	0.51699	0.053
57DAP/7DAP	1.08567	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8704	0.122
17DAP/reference	0.74166	0.024
27DAP/reference	0.82576	0.071
39DAP/reference	0.73775	0.023
41DAP/reference	0.92582	0.326
42DAP/reference	0.61355	0.01
43DAP/reference	0.66685	0.012
47DAP/reference	0.94514	0.504
52DAP/reference	0.77004	0.035
57DAP/reference	0.70337	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02225	0.832
17DAP/reference	1.5133	0.013
27DAP/reference	1.67398	0.02
39DAP/reference	1.29737	0.054
41DAP/reference	1.38682	0.01
42DAP/reference	1.3384	0.031
43DAP/reference	1.44083	0.149
47DAP/reference	1.64583	0.01
52DAP/reference	1.38084	0.014
57DAP/reference	1.29693	0.101

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74487	0.035
17DAP/reference	1.04603	1
27DAP/reference	0.92194	0.195
39DAP/reference	0.8575	0.069
41DAP/reference	0.99326	0.618
42DAP/reference	1.09168	0.45
43DAP/reference	1.23357	0.452
47DAP/reference	1.21924	0.171
52DAP/reference	1.08252	0.664
57DAP/reference	1.24182	0.462

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14987	0.966
26DAP/20DAP	1.11208	0.785
34DAP/26DAP	0.93164	0.944
51DAP/34DAP	1.28555	0.429
52DAP/51DAP	1.08978	1
53DAP/52DAP	1.22159	0.565
55DAP/53DAP	1.05004	0.917
57DAP/55DAP	0.94313	0.748
62DAP/57DAP	0.9473	0.871
68DAP/62DAP	1.0892	0.821
68DAP/14DAP	0.70098	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.41061	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.43704	0.417
Mature Green Tomato/Ripe Tomato	0.1347	0.017
Immature Eggplant/Mature Eggplant	1.46115	0.05
Ripe Pepper/Ripe Tomato	0.25634	0.293
Mature Eggplant/Ripe Tomato	0.17233	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09188	1
1-1-2/M82	1.17462	0.977
12-2/M82	1.56874	1
12-4/M82	1.89987	1
1-3/M82	2.22883	1
2-1-1/M82	1.35667	0.439
2-1/M82	0.65763	0.322
2-6/M82	0.90583	1
3-2/M82	1.72715	0.84
4-1-1/M82	1.55124	0.968
4-1/M82	0.56141
4-3-2/M82	1.64408	0.253
4-3/M82	2.04122	0.268
5-3/M82	1.47407	0.496
6-2/M82	2.6151
6-3/M82	1.56851	1
7-1/M82	0.83176	0.443
7-2/M82	1.7491	0.318
9-3-2/M82	2.0501	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03012
IL2-6/WTpooled	0.97938	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10826	1
IL12-4/WTpooled	0.73377	0.461
IL1-4/WTpooled	1.02974	1
WT/WTpooled	1.01844	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	1.74577	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94294	1
DC3000/delta hrp 6h	0.84504	0.95
DC3000/delta hrp 12h	0.91358	1
DC3000/delta hrp 24h	1.45927	0.063

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17919	0.333
DC3000 delta B/DC3000 delta AB	1.68897	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86571	1
Exp 36h	1.49515	0.489
Exp 60h	1.43563	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96232	1
Var 0h	1.9901	0.782
Var 12h I row2-row1	1.07815	0.692
Var 12h NI row2-row1	0.94956	0.906
Var 36h I row2-row1	0.79709	0.805
Var 36h NI row2-row1	0.91671	0.743
Var 60h I row2-row1	0.95661	0.952
Var 60h NI row2-row1	1.01335	1
Time course 0hI-0hNI	0.84675	0.101
Time course 12hI-12hNI	0.81937	0.033
Time course 36hI-36hNI	1.04834	0.718
Time course 60hI-60hNI	1.82241	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)	0.96732	0.26
transgenic ySAMdc/azygous control (breaker)	2.73757	0.165
transgenic ySAMdc/azygous control (red)	1.5933	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00204	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96959	0.431

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.56878	0.172
Manapal/WT (break)	0.91237	1
Manapal/WT (red)	0.36387	0.181