Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.62154	0.085
27DAP/17DAP	0.86667	0.609
39DAP/27DAP	0.70909	0.315
41DAP/39DAP	1.07881	0.612
42DAP/41DAP	1.40128	0.236
43DAP/42DAP	1.01007	0.937
47DAP/43DAP	1.0835	0.884
52DAP/47DAP	0.77931	0.455
57DAP/52DAP	1.15017	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91839	0.293
17DAP/reference	0.94914	0.321
27DAP/reference	1.05601	0.415
39DAP/reference	0.97804	0.68
41DAP/reference	0.8829	0.049
42DAP/reference	0.98176	0.384
43DAP/reference	1.01032	0.928
47DAP/reference	0.99629	0.636
52DAP/reference	1.02147	0.951
57DAP/reference	1.04247	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00442	0.899
27DAP/17DAP	1.03702	0.872
39DAP/27DAP	0.98705	0.932
41DAP/39DAP	1.00919	1
42DAP/41DAP	1.03586	0.935
43DAP/42DAP	1.0429	0.699
47DAP/43DAP	1.05116	0.772
52DAP/47DAP	1.03624	0.862
57DAP/52DAP	0.94388	0.531
57DAP/7DAP	1.08444	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80298	0.088
17DAP/reference	0.76508	0.011
27DAP/reference	0.73425	0.01
39DAP/reference	0.8582	0.064
41DAP/reference	0.90003	0.194
42DAP/reference	0.83864	0.028
43DAP/reference	0.73578	0.054
47DAP/reference	0.87539	0.383
52DAP/reference	0.679	0.012
57DAP/reference	0.78586	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97228	0.655
17DAP/reference	0.84136	0.011
27DAP/reference	0.84009	0.097
39DAP/reference	0.93387	0.165
41DAP/reference	0.96997	0.331
42DAP/reference	0.83203	0.039
43DAP/reference	0.82638	0.04
47DAP/reference	0.93014	0.061
52DAP/reference	1.04189	0.368
57DAP/reference	0.91574	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79735	0.074
17DAP/reference	0.88762	0.275
27DAP/reference	0.69084	0.036
39DAP/reference	0.71571	0.024
41DAP/reference	0.90328	0.148
42DAP/reference	0.78649	0.059
43DAP/reference	0.81643	0.043
47DAP/reference	1.17093	0.14
52DAP/reference	0.70322	0.096
57DAP/reference	1.12781	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.32073	0.786
26DAP/20DAP	1.01847	1
34DAP/26DAP	0.95125	0.893
51DAP/34DAP	1.53727	0.032
52DAP/51DAP	1.09298	0.708
53DAP/52DAP	1.22756	0.187
55DAP/53DAP	1.07526	0.771
57DAP/55DAP	0.8666	0.313
62DAP/57DAP	1.0956	0.723
68DAP/62DAP	1.16666	0.565
68DAP/14DAP	1.33435	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.69303	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.3313	0.058
Mature Green Tomato/Ripe Tomato	1.23633	0.267
Immature Eggplant/Mature Eggplant	0.87205	0.808
Ripe Pepper/Ripe Tomato	4.55799	1
Mature Eggplant/Ripe Tomato	4.62642	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.06539
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.16349	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.65156

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74059	0.243
IL2-6/WTpooled	0.6385	0.473
IL7-5/WTpooled	0.64602	1
IL7-3/WTpooled	0.88013	1
IL12-4/WTpooled	0.86862	0.71
IL1-4/WTpooled	1.03417	1
WT/WTpooled	0.92434	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	0.88751	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12278	0.875
DC3000/delta hrp 6h	0.91682	0.95
DC3000/delta hrp 12h	1.01262	1
DC3000/delta hrp 24h	0.35148	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.70663	0.039
DC3000 delta B/DC3000 delta AB	0.78211	0.037

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90012	1
Exp 36h	0.86361	0.749
Exp 60h	0.7886	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96761	1
Var 0h	0.88986	0.933
Var 12h I row2-row1	0.83632	0.418
Var 12h NI row2-row1	0.97753	0.906
Var 36h I row2-row1	1.00226	1
Var 36h NI row2-row1	1.17353	1
Var 60h I row2-row1	1.2368	0.562
Var 60h NI row2-row1	1.10029	0.904
Time course 0hI-0hNI	0.97106	0.873
Time course 12hI-12hNI	0.9297	0.368
Time course 36hI-36hNI	0.89677	0.179
Time course 60hI-60hNI	0.28103	0.005

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)	1.3065	0.289
transgenic ySAMdc/azygous control (breaker)	1.25325	0.248
transgenic ySAMdc/azygous control (red)	1.10614	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97224	0.237

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.82305	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.31693	0.088
Manapal/WT (break)	5.64085	0.126
Manapal/WT (red)	1.87753	0.222