Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.3.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90866	0.543
27DAP/17DAP	1.75383	0.758
39DAP/27DAP	1.12915	0.985
41DAP/39DAP	1.00826	0.939
42DAP/41DAP	1.2175	1
43DAP/42DAP	1.01979	0.937
47DAP/43DAP	1.13357	0.727
52DAP/47DAP	0.8422	0.586
57DAP/52DAP	1.09554	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97436	0.539
17DAP/reference	0.87982	0.06
27DAP/reference	1.11937	0.291
39DAP/reference	0.80016	0.019
41DAP/reference	0.78822	0.008
42DAP/reference	0.94338	0.103
43DAP/reference	1.01272	0.957
47DAP/reference	1.02453	0.84
52DAP/reference	1.10882	0.286
57DAP/reference	1.19985	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98096	0.732
27DAP/17DAP	1.18927	0.768
39DAP/27DAP	0.92338	0.572
41DAP/39DAP	1.65183	0.59
42DAP/41DAP	0.76734	0.086
43DAP/42DAP	0.80413	0.116
47DAP/43DAP	1.7196	0.906
52DAP/47DAP	1.16066	0.549
57DAP/52DAP	1.74466	0.33
57DAP/7DAP	0.68302

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08062	0.338
17DAP/reference	1.03054	0.971
27DAP/reference	0.9504	0.248
39DAP/reference	1.05809	0.511
41DAP/reference	1.13362	0.402
42DAP/reference	1.0599	0.889
43DAP/reference	1.57582	0.007
47DAP/reference	1.28493	0.014
52DAP/reference	1.71533	0.008
57DAP/reference	1.40666	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06994	0.634
17DAP/reference	0.87475	0.153
27DAP/reference	1.00374	0.79
39DAP/reference	0.97422	0.37
41DAP/reference	1.09138	0.614
42DAP/reference	0.89014	0.15
43DAP/reference	0.8615	0.147
47DAP/reference	0.89326	0.12
52DAP/reference	0.92534	0.121
57DAP/reference	0.80431	0.04

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45386	0.045
17DAP/reference	0.91211	0.308
27DAP/reference	1.07213	0.408
39DAP/reference	0.98177	0.464
41DAP/reference	0.86808	0.058
42DAP/reference	0.96119	0.552
43DAP/reference	1.14202	0.412
47DAP/reference	1.14291	0.133
52DAP/reference	1.21225	0.318
57DAP/reference	1.19675	0.151

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92044	0.997
26DAP/20DAP	1.36448	0.369
34DAP/26DAP	1.15874	1
51DAP/34DAP	1.22564	0.759
52DAP/51DAP	0.9239	1
53DAP/52DAP	1.02473	0.902
55DAP/53DAP	0.9497	0.619
57DAP/55DAP	1.50368	1
62DAP/57DAP	1.41573	0.902
68DAP/62DAP	1.27604	0.664
68DAP/14DAP	1.39459	0.069

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17943	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.50402	0.058
Mature Green Tomato/Ripe Tomato	1.36647	0.632
Immature Eggplant/Mature Eggplant	1.76782	0.05
Ripe Pepper/Ripe Tomato	1.28111	1
Mature Eggplant/Ripe Tomato	0.78521	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03192	0.877
1-1-2/M82	1.0068	1
12-2/M82	1.06719	1
12-4/M82	1.04626	1
1-3/M82	0.96112	1
2-1-1/M82	1.05547	0.457
2-1/M82	1.43426	1
2-6/M82	1.04796	0.695
3-2/M82	1.02084
4-1-1/M82	0.91675	1
4-1/M82	1.05306
4-3-2/M82	1.04325	0.262
4-3/M82	0.94237	1
5-3/M82	0.901	1
6-2/M82	1.10649	1
6-3/M82	0.96601	1
7-1/M82	1.07777	1
7-2/M82	1.01273	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.80227	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.54859	0.362
IL12-4/WTpooled	1.08275	0.839
IL1-4/WTpooled	1.02879
WT/WTpooled	1.07062	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	0.76127	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94482	1
DC3000/delta hrp 6h	0.8453	0.95
DC3000/delta hrp 12h	0.89081	1
DC3000/delta hrp 24h	1.09511	0.221

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10828
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06836	1
Exp 36h	1.28785	0.693
Exp 60h	1.46049	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92175
Var 0h	0.87437	1
Var 12h I row2-row1	1.3084	0.613
Var 12h NI row2-row1	1.20963	0.649
Var 36h I row2-row1	1.12417	1
Var 36h NI row2-row1	1.18934	0.253
Var 60h I row2-row1	0.97264
Var 60h NI row2-row1	1.30635	0.691
Time course 0hI-0hNI	1.10645	0.764
Time course 12hI-12hNI	1.14812	0.65
Time course 36hI-36hNI	0.9051	0.337
Time course 60hI-60hNI	0.48245	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)	1.00935	1
transgenic ySAMdc/azygous control (breaker)	0.46686	0.122
transgenic ySAMdc/azygous control (red)	1.69092	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14494	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.61808	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.46855	0.093
Manapal/WT (break)	1.29198	1
Manapal/WT (red)	1.21007	0.413