Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23074	0.523
27DAP/17DAP	1.45512	0.613
39DAP/27DAP	1.57113	0.061
41DAP/39DAP	0.81557	0.396
42DAP/41DAP	0.91121	1
43DAP/42DAP	1.35478	0.512
47DAP/43DAP	1.23033	0.253
52DAP/47DAP	1.16699	0.816
57DAP/52DAP	1.69331	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18664	0.078
17DAP/reference	0.87121	0.158
27DAP/reference	0.90848	0.385
39DAP/reference	0.85444	0.07
41DAP/reference	0.76652	0.012
42DAP/reference	1.14266	0.003
43DAP/reference	0.96723	0.675
47DAP/reference	1.20278	0.011
52DAP/reference	1.12588	0.388
57DAP/reference	1.23922	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0253	0.871
27DAP/17DAP	1.3614	0.05
39DAP/27DAP	1.25949	0.249
41DAP/39DAP	1.23344	0.674
42DAP/41DAP	1.2056	0.072
43DAP/42DAP	1.34884	0.061
47DAP/43DAP	1.02152	0.956
52DAP/47DAP	0.86956	0.29
57DAP/52DAP	1.10916	0.451
57DAP/7DAP	1.05929	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21588	0.044
17DAP/reference	1.10004	0.092
27DAP/reference	0.96993	0.402
39DAP/reference	1.03356	1
41DAP/reference	1.20917	0.024
42DAP/reference	1.19631	0.021
43DAP/reference	1.10324	0.167
47DAP/reference	1.256	0.173
52DAP/reference	1.20961	0.038
57DAP/reference	1.21225	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08618	0.758
17DAP/reference	1.23354	0.131
27DAP/reference	1.53159	0.035
39DAP/reference	1.2583	0.194
41DAP/reference	1.16548	0.038
42DAP/reference	1.31175	0.064
43DAP/reference	1.05985	1
47DAP/reference	1.23775	0.101
52DAP/reference	1.08984	0.3
57DAP/reference	0.93389	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16617	0.212
17DAP/reference	0.98331	0.696
27DAP/reference	1.06737	0.51
39DAP/reference	1.15743	0.087
41DAP/reference	1.01742	1
42DAP/reference	1.25083	0.154
43DAP/reference	1.09351	0.432
47DAP/reference	1.03578	0.934
52DAP/reference	1.60489	0.041
57DAP/reference	1.63016	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10383	0.966
26DAP/20DAP	1.45864	0.288
34DAP/26DAP	1.69528	0.304
51DAP/34DAP	2.17149	0.026
52DAP/51DAP	0.89953	1
53DAP/52DAP	0.65614	0.066
55DAP/53DAP	0.4102	0.017
57DAP/55DAP	1.11844	0.969
62DAP/57DAP	0.95703	1
68DAP/62DAP	1.07997	0.897
68DAP/14DAP	1.38638	0.077

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.28662	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94781	0.635
Mature Green Tomato/Ripe Tomato	0.55301	0.055
Immature Eggplant/Mature Eggplant	0.8978	0.176
Ripe Pepper/Ripe Tomato	1.58215	1
Mature Eggplant/Ripe Tomato	0.40522	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.57107	0.587
1-1-2/M82	0.64324
12-2/M82	N/A	N/A
12-4/M82	0.72381	0.282
1-3/M82	1.47739
2-1-1/M82	N/A	N/A
2-1/M82	0.90394	0.519
2-6/M82	0.6589	1
3-2/M82	N/A	N/A
4-1-1/M82	0.60867	1
4-1/M82	0.55862
4-3-2/M82	N/A	N/A
4-3/M82	0.6188
5-3/M82	1.16977	1
6-2/M82	0.95823
6-3/M82	0.79741	1
7-1/M82	1.23633
7-2/M82	1.30851	0.299
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	1.18094	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96636	1
IL12-4/WTpooled	1.49088	0.553
IL1-4/WTpooled	0.62068
WT/WTpooled	0.98133	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	1.06583	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9962	1
DC3000/delta hrp 6h	1.00351	0.95
DC3000/delta hrp 12h	1.01605	1
DC3000/delta hrp 24h	0.85387	0.22

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.61057
DC3000 delta B/DC3000 delta AB	1.26527	0.193

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96809	1
Var 0h	0.88752	0.933
Var 12h I row2-row1	1.01437	1
Var 12h NI row2-row1	0.97522	0.906
Var 36h I row2-row1	1.02138	1
Var 36h NI row2-row1	1.04571	1
Var 60h I row2-row1	0.91119	0.832
Var 60h NI row2-row1	0.8046	0.458
Time course 0hI-0hNI	1.05168	0.574
Time course 12hI-12hNI	1.09384	0.143
Time course 36hI-36hNI	1.51002	0.005
Time course 60hI-60hNI	1.38821	0.011

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)	1.15257	0.289
transgenic ySAMdc/azygous control (breaker)	0.90904	1
transgenic ySAMdc/azygous control (red)	0.86243	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.86304	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7815	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93523	1
Manapal/WT (break)	1.13495	0.381
Manapal/WT (red)	2.84392	0.15