Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.11.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60302	0.094
27DAP/17DAP	0.91169	0.807
39DAP/27DAP	1.71617	0.113
41DAP/39DAP	1.04242	0.859
42DAP/41DAP	1.32785	0.361
43DAP/42DAP	0.50791	0.454
47DAP/43DAP	0.60852	0.105
52DAP/47DAP	0.97787	0.861
57DAP/52DAP	1.0954	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9633	0.489
17DAP/reference	1.31833	0.049
27DAP/reference	1.12727	0.038
39DAP/reference	1.06509	0.352
41DAP/reference	1.13761	0.111
42DAP/reference	0.98354	0.413
43DAP/reference	0.95295	0.377
47DAP/reference	0.92483	0.137
52DAP/reference	0.74665	0.033
57DAP/reference	0.7988	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.20823	0.054
27DAP/17DAP	0.55927	0.158
39DAP/27DAP	2.19606	0.044
41DAP/39DAP	0.70419	0.093
42DAP/41DAP	1.48781	0.032
43DAP/42DAP	1.0066	0.83
47DAP/43DAP	0.56059	0.008
52DAP/47DAP	1.20367	0.512
57DAP/52DAP	0.60167	0.092
57DAP/7DAP	0.75985	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8996	0.031
17DAP/reference	0.75711	0.013
27DAP/reference	0.95378	0.325
39DAP/reference	1.44111	0.01
41DAP/reference	0.72092	0.016
42DAP/reference	0.86288	0.151
43DAP/reference	0.67334	0.02
47DAP/reference	0.71975	0.079
52DAP/reference	0.72983	0.023
57DAP/reference	0.58823	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08573	0.279
17DAP/reference	1.08121	0.496
27DAP/reference	0.88869	0.111
39DAP/reference	1.49312	0.03
41DAP/reference	0.91868	0.188
42DAP/reference	0.96522	0.392
43DAP/reference	0.89206	0.196
47DAP/reference	0.96112	0.328
52DAP/reference	0.905	0.156
57DAP/reference	0.87902	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15426	0.153
17DAP/reference	0.88178	0.239
27DAP/reference	0.82274	0.063
39DAP/reference	0.88092	0.111
41DAP/reference	1.13202	0.174
42DAP/reference	0.85937	0.287
43DAP/reference	0.74873	0.081
47DAP/reference	0.88852	0.145
52DAP/reference	0.99387	0.69
57DAP/reference	0.66009	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02419	1
26DAP/20DAP	0.73623	0.317
34DAP/26DAP	0.81003	0.44
51DAP/34DAP	1.25399	0.829
52DAP/51DAP	0.84523	1
53DAP/52DAP	1.23067	0.594
55DAP/53DAP	0.88758	0.577
57DAP/55DAP	1.21522	0.854
62DAP/57DAP	0.89244	0.871
68DAP/62DAP	0.77974	0.118
68DAP/14DAP	0.59377	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.57713	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11043	0.417
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	4.08376	0.045
Ripe Pepper/Ripe Tomato	2.10792	0.256
Mature Eggplant/Ripe Tomato	3.53389	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96045	0.944
1-1-2/M82	0.96341	1
12-2/M82	N/A	N/A
12-4/M82	0.9667	1
1-3/M82	N/A	N/A
2-1-1/M82	1.74197
2-1/M82	N/A	N/A
2-6/M82	0.79785
3-2/M82	0.9538	0.455
4-1-1/M82	0.51215	1
4-1/M82	0.83044	0.737
4-3-2/M82	0.96387	1
4-3/M82	1.06822	1
5-3/M82	1.12523	0.455
6-2/M82	1.02017
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.92148
9-3-2/M82	1.23607	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94027	1
IL7-5/WTpooled	0.93671
IL7-3/WTpooled	1.09928	1
IL12-4/WTpooled	0.91412	0.71
IL1-4/WTpooled	1.05135	1
WT/WTpooled	1.03467	0.874

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	1.11753	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99837
DC3000/delta hrp 6h	1.08599	1
DC3000/delta hrp 12h	1.51748
DC3000/delta hrp 24h	0.55365	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.72296	0.035
DC3000 delta B/DC3000 delta AB	0.85915	0.253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84481	0.245
Exp 36h	0.68242	0.406
Exp 60h	0.81882	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96108	1
Var 0h	0.90891	0.237
Var 12h I row2-row1	0.84366	0.338
Var 12h NI row2-row1	1.0879	0.34
Var 36h I row2-row1	1.06101	1
Var 36h NI row2-row1	1.16276	1
Var 60h I row2-row1	0.99194	1
Var 60h NI row2-row1	1.08725	0.904
Time course 0hI-0hNI	1.11069	0.764
Time course 12hI-12hNI	0.84958	0.101
Time course 36hI-36hNI	0.79988	0.023
Time course 60hI-60hNI	0.3151	0.006

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)	1.0004	1
transgenic ySAMdc/azygous control (breaker)	1.42	0.248
transgenic ySAMdc/azygous control (red)	1.03497	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99564	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.57332	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.50308	0.172
Manapal/WT (break)	0.68241	0.299
Manapal/WT (red)	0.73236	0.181