Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.6.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85938	0.389
27DAP/17DAP	1.14393	0.859
39DAP/27DAP	0.97411	0.719
41DAP/39DAP	1.23692	0.357
42DAP/41DAP	1.64007	0.079
43DAP/42DAP	0.91298	0.801
47DAP/43DAP	0.7984	0.41
52DAP/47DAP	1.28494	0.538
57DAP/52DAP	0.86203	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12068	0.48
17DAP/reference	0.96912	0.664
27DAP/reference	0.74387	0.055
39DAP/reference	1.06433	0.581
41DAP/reference	0.93841	0.341
42DAP/reference	1.26063	0.026
43DAP/reference	1.39581	0.008
47DAP/reference	1.10239	0.215
52DAP/reference	1.10511	0.633
57DAP/reference	1.15881	0.229

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99313	0.801
27DAP/17DAP	1.03854	0.915
39DAP/27DAP	1.15236	0.096
41DAP/39DAP	0.99133	0.997
42DAP/41DAP	1.08557	0.861
43DAP/42DAP	1.14473	0.112
47DAP/43DAP	1.09764	0.779
52DAP/47DAP	1.0514	0.835
57DAP/52DAP	1.08948	0.611
57DAP/7DAP	1.44732	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82074	0.129
17DAP/reference	0.74797	0.011
27DAP/reference	0.80338	0.01
39DAP/reference	0.75962	0.011
41DAP/reference	0.72079	0.012
42DAP/reference	0.76711	0.01
43DAP/reference	0.70332	0.011
47DAP/reference	1.19715	0.761
52DAP/reference	0.66355	0.013
57DAP/reference	0.72934	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10496	0.55
17DAP/reference	1.20711	0.028
27DAP/reference	1.09588	0.781
39DAP/reference	0.82498	0.165
41DAP/reference	0.73412	0.073
42DAP/reference	1.09433	0.359
43DAP/reference	1.03296	0.863
47DAP/reference	1.15762	0.247
52DAP/reference	0.84788	0.187
57DAP/reference	0.86131	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83066	0.071
17DAP/reference	0.91045	0.308
27DAP/reference	0.7408	0.03
39DAP/reference	0.69297	0.01
41DAP/reference	0.79202	0.023
42DAP/reference	0.91979	0.287
43DAP/reference	0.91433	0.116
47DAP/reference	0.90775	0.207
52DAP/reference	0.92124	0.493
57DAP/reference	0.91216	0.299

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00726	1
26DAP/20DAP	0.85231	0.244
34DAP/26DAP	0.94283	0.841
51DAP/34DAP	0.92785	0.624
52DAP/51DAP	1.15618	0.413
53DAP/52DAP	0.94148	0.572
55DAP/53DAP	1.02761	0.806
57DAP/55DAP	1.07034	0.87
62DAP/57DAP	0.48085	0.003
68DAP/62DAP	1.51322	0.413
68DAP/14DAP	2.24668	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.97029	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.53743	0.106
Mature Green Tomato/Ripe Tomato	0.70038	0.047
Immature Eggplant/Mature Eggplant	1.5261	0.05
Ripe Pepper/Ripe Tomato	1.60374	1
Mature Eggplant/Ripe Tomato	0.89975	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03532	1
1-1-2/M82	0.94805	1
12-2/M82	1.11269	1
12-4/M82	1.28492	0.611
1-3/M82	0.87955	0.441
2-1-1/M82	1.53717
2-1/M82	1.14953
2-6/M82	1.18411	0.364
3-2/M82	1.12541
4-1-1/M82	0.92786	1
4-1/M82	0.92682
4-3-2/M82	N/A	N/A
4-3/M82	2.35108	0.268
5-3/M82	0.90847	0.642
6-2/M82	N/A	N/A
6-3/M82	0.87516	1
7-1/M82	0.7919	0.509
7-2/M82	1.02985	1
9-3-2/M82	1.35998

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72602	0.243
IL2-6/WTpooled	1.60462	0.46
IL7-5/WTpooled	0.81309	1
IL7-3/WTpooled	0.69967	0.298
IL12-4/WTpooled	0.94322	1
IL1-4/WTpooled	0.79627	0.415
WT/WTpooled	1.04421	0.999

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	1.04415	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96656	0.941
DC3000/delta hrp 6h	0.85855	0.95
DC3000/delta hrp 12h	0.9617	1
DC3000/delta hrp 24h	1.36966	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.8205	0.445

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1072	1
Exp 36h	1.56512	0.693
Exp 60h	2.02713	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03118	1
Var 0h	1.07133	1
Var 12h I row2-row1	1.1245	0.613
Var 12h NI row2-row1	0.97389	1
Var 36h I row2-row1	0.91781	0.805
Var 36h NI row2-row1	0.90617	0.645
Var 60h I row2-row1	1.09725	1
Var 60h NI row2-row1	1.27417	0.904
Time course 0hI-0hNI	1.11488	0.662
Time course 12hI-12hNI	1.06234	0.567
Time course 36hI-36hNI	1.03744	0.722
Time course 60hI-60hNI	1.55663	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)	0.95534	0.567
transgenic ySAMdc/azygous control (breaker)	1.27493	0.178
transgenic ySAMdc/azygous control (red)	1.26352	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96624	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86903	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76902	1
Manapal/WT (break)	1.39507	0.381
Manapal/WT (red)	0.89128	0.229