Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.9.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.53442	0.033
27DAP/17DAP	0.61519	0.066
39DAP/27DAP	2.16196	0.055
41DAP/39DAP	1.0589	0.871
42DAP/41DAP	1.57857	0.207
43DAP/42DAP	0.39361	0.409
47DAP/43DAP	0.37926	0.049
52DAP/47DAP	0.79005	0.581
57DAP/52DAP	1.00652	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92537	0.284
17DAP/reference	1.23873	0.294
27DAP/reference	1.25749	0.05
39DAP/reference	1.20699	0.02
41DAP/reference	1.10115	0.073
42DAP/reference	1.01283	0.531
43DAP/reference	0.87303	0.016
47DAP/reference	0.90217	0.148
52DAP/reference	0.89405	0.121
57DAP/reference	0.8855	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.45475	0.04
27DAP/17DAP	0.47752	0.101
39DAP/27DAP	2.56604	0.044
41DAP/39DAP	0.76388	0.276
42DAP/41DAP	1.379	0.091
43DAP/42DAP	0.94711	0.597
47DAP/43DAP	0.54213	0.008
52DAP/47DAP	1.18919	0.527
57DAP/52DAP	0.40781	0.049
57DAP/7DAP	0.63037	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19987	0.119
17DAP/reference	1.05082	0.477
27DAP/reference	1.61289	0.008
39DAP/reference	1.48457	0.006
41DAP/reference	1.07751	0.35
42DAP/reference	1.31823	0.018
43DAP/reference	0.94465	0.351
47DAP/reference	1.01782	1
52DAP/reference	1.09445	0.459
57DAP/reference	0.69911	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12128	0.33
17DAP/reference	1.25906	0.07
27DAP/reference	1.74712	0.014
39DAP/reference	2.68955	0.011
41DAP/reference	1.28782	0.017
42DAP/reference	1.45469	0.013
43DAP/reference	1.69296	0.029
47DAP/reference	1.35004	0.014
52DAP/reference	1.40578	0.006
57DAP/reference	1.306	0.029

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00372	0.804
17DAP/reference	1.00019	0.81
27DAP/reference	1.29739	0.022
39DAP/reference	1.31908	0.013
41DAP/reference	1.52727	0.02
42DAP/reference	1.54723	0.013
43DAP/reference	1.0356	0.721
47DAP/reference	0.9338	0.224
52DAP/reference	1.41929	0.216
57DAP/reference	1.07012	0.539

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95939	1
26DAP/20DAP	0.73097	0.317
34DAP/26DAP	0.8189	0.322
51DAP/34DAP	1.10101	0.869
52DAP/51DAP	1.13155	0.965
53DAP/52DAP	0.96528	0.876
55DAP/53DAP	3.26158	0.537
57DAP/55DAP	0.80145	0.375
62DAP/57DAP	1.05594	0.8
68DAP/62DAP	0.79587	0.152
68DAP/14DAP	0.62898	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	10.7063	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.90444	0.058
Mature Green Tomato/Ripe Tomato	31.6142	0.014
Immature Eggplant/Mature Eggplant	9.91392	0.05
Ripe Pepper/Ripe Tomato	2.42748	1
Mature Eggplant/Ripe Tomato	7.95785	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.74398
12-2/M82	1.21624
12-4/M82	1.34127
1-3/M82	0.51498
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	1.11076	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.9969
9-3-2/M82	1.02085

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.49946	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.59441
IL12-4/WTpooled	1.18871	0.516
IL1-4/WTpooled	0.64661	0.457
WT/WTpooled	0.97637	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	1.15104	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0093	1
DC3000/delta hrp 6h	1.33527	1
DC3000/delta hrp 12h	1.10426	1
DC3000/delta hrp 24h	0.49406	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68001	0.023
DC3000 delta B/DC3000 delta AB	0.69149	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90858	0.328
Exp 36h	0.82038	0.449
Exp 60h	0.78305	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01246	1
Var 0h	0.97758	1
Var 12h I row2-row1	0.9017	0.353
Var 12h NI row2-row1	1.1538	1
Var 36h I row2-row1	1.22447	0.309
Var 36h NI row2-row1	0.97292	0.743
Var 60h I row2-row1	1.02613	1
Var 60h NI row2-row1	1.05828	1
Time course 0hI-0hNI	1.04095	0.867
Time course 12hI-12hNI	0.88839	0.255
Time course 36hI-36hNI	0.89665	0.095
Time course 60hI-60hNI	0.57438	0.026

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)	0.9782	0.789
transgenic ySAMdc/azygous control (breaker)	1.25092	1
transgenic ySAMdc/azygous control (red)	1.47767	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14847	0.033

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.3634	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.36469	0.172
Manapal/WT (break)	0.44658	0.299
Manapal/WT (red)	0.59844	0.229