Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.13.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03678	0.904
27DAP/17DAP	1.02269	1
39DAP/27DAP	0.95472	0.594
41DAP/39DAP	1.05015	0.992
42DAP/41DAP	1.09591	0.888
43DAP/42DAP	1.08403	0.968
47DAP/43DAP	1.02194	1
52DAP/47DAP	0.86593	0.627
57DAP/52DAP	1.11516	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97302	0.661
17DAP/reference	0.97898	0.777
27DAP/reference	0.89204	0.013
39DAP/reference	0.91737	0.103
41DAP/reference	1.02219	0.516
42DAP/reference	0.96456	0.242
43DAP/reference	0.96974	0.5
47DAP/reference	0.98066	0.445
52DAP/reference	1.05775	0.286
57DAP/reference	1.01548	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03531	0.619
27DAP/17DAP	1.01191	0.968
39DAP/27DAP	0.97396	0.721
41DAP/39DAP	1.00723	0.895
42DAP/41DAP	0.98523	0.845
43DAP/42DAP	1.05266	0.112
47DAP/43DAP	1.01616	0.884
52DAP/47DAP	0.98301	0.925
57DAP/52DAP	0.97469	0.68
57DAP/7DAP	1.14163

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80809	0.078
17DAP/reference	0.81135	0.012
27DAP/reference	0.88481	0.014
39DAP/reference	0.73031	0.011
41DAP/reference	0.69812	0.015
42DAP/reference	0.72867	0.011
43DAP/reference	0.67371	0.012
47DAP/reference	0.75253	0.038
52DAP/reference	0.65693	0.012
57DAP/reference	0.66087	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02414	0.719
17DAP/reference	1.08078	0.448
27DAP/reference	1.03358	0.765
39DAP/reference	0.89556	0.077
41DAP/reference	0.80436	0.04
42DAP/reference	0.91383	0.121
43DAP/reference	1.11798	0.532
47DAP/reference	0.97915	0.487
52DAP/reference	0.87688	0.008
57DAP/reference	1.01723	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79599	0.026
17DAP/reference	0.93806	0.508
27DAP/reference	0.78149	0.021
39DAP/reference	0.76869	0.011
41DAP/reference	0.80082	0.025
42DAP/reference	0.83229	0.071
43DAP/reference	0.81607	0.022
47DAP/reference	0.86374	0.093
52DAP/reference	0.89468	0.351
57DAP/reference	0.72934	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02789	0.966
26DAP/20DAP	1.0464	0.839
34DAP/26DAP	1.02245	1
51DAP/34DAP	1.01336	0.962
52DAP/51DAP	0.99873	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	N/A	N/A
57DAP/55DAP	1.05331	0.745
62DAP/57DAP	1.03627	0.868
68DAP/62DAP	0.88113	0.787
68DAP/14DAP	1.14118	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10033	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85977
Mature Green Tomato/Ripe Tomato	1.01794	1
Immature Eggplant/Mature Eggplant	1.12702	0.485
Ripe Pepper/Ripe Tomato	1.26165	1
Mature Eggplant/Ripe Tomato	2.05563	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95299	0.944
1-1-2/M82	0.98631	1
12-2/M82	0.97232	0.955
12-4/M82	0.94329	0.619
1-3/M82	0.9364	0.501
2-1-1/M82	0.82207	0.465
2-1/M82	1.33576	1
2-6/M82	0.94916	1
3-2/M82	0.98491	0.752
4-1-1/M82	1.01811	1
4-1/M82	0.89524	0.737
4-3-2/M82	0.75375	0.487
4-3/M82	0.86641	0.72
5-3/M82	1.01376	1
6-2/M82	0.94535	1
6-3/M82	1.02299	1
7-1/M82	1.0451
7-2/M82	0.89792	0.796
9-3-2/M82	0.84791	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.99934	0.365
IL2-6/WTpooled	0.58622	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10861	1
IL12-4/WTpooled	1.13964	0.785
IL1-4/WTpooled	1.08271	1
WT/WTpooled	1.07682	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	0.84508	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02563	0.921
DC3000/delta hrp 6h	1.37858	1
DC3000/delta hrp 12h	1.03045	1
DC3000/delta hrp 24h	1.07701	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08083	0.183
DC3000 delta B/DC3000 delta AB	1.0597	0.479

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	0.8533	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00944	1
Var 0h	1.07838	0.98
Var 12h I row2-row1	1.14976	0.187
Var 12h NI row2-row1	1.04474	1
Var 36h I row2-row1	0.86871	0.805
Var 36h NI row2-row1	0.99191	0.852
Var 60h I row2-row1	1.13844	0.562
Var 60h NI row2-row1	1.03024	1
Time course 0hI-0hNI	1.06375	0.852
Time course 12hI-12hNI	1.01035	1
Time course 36hI-36hNI	0.94358	0.38
Time course 60hI-60hNI	0.96035	0.646

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)	0.9344	0.567
transgenic ySAMdc/azygous control (breaker)	1.34164	1
transgenic ySAMdc/azygous control (red)	1.49387	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91889	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09544	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01083	1
Manapal/WT (break)	0.53787	0.236
Manapal/WT (red)	0.99835	1