Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97851	0.752
27DAP/17DAP	1.98911	0.208
39DAP/27DAP	3.83695	0.02
41DAP/39DAP	1.35499	0.591
42DAP/41DAP	1.17851	0.772
43DAP/42DAP	1.31389	0.505
47DAP/43DAP	1.73406	0.187
52DAP/47DAP	0.79782	0.502
57DAP/52DAP	2.13696	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5688	0.027
17DAP/reference	0.50917	0.007
27DAP/reference	0.69144	0.017
39DAP/reference	1.26903	0.786
41DAP/reference	0.75908	0.065
42DAP/reference	1.40824	0.016
43DAP/reference	1.23939	0.031
47DAP/reference	2.59779	0.001
52DAP/reference	1.51386	0.019
57DAP/reference	1.43471	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19836	0.326
27DAP/17DAP	1.16025	0.724
39DAP/27DAP	2.44103	0.06
41DAP/39DAP	0.54716	0.169
42DAP/41DAP	0.97542	0.753
43DAP/42DAP	0.97751	0.854
47DAP/43DAP	1.2787	0.471
52DAP/47DAP	0.9765	0.886
57DAP/52DAP	1.35931	0.533
57DAP/7DAP	2.78554	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54286	0.052
17DAP/reference	0.43932	0.011
27DAP/reference	0.75744	0.035
39DAP/reference	0.94836	0.354
41DAP/reference	1.25263	0.141
42DAP/reference	1.30191	0.059
43DAP/reference	1.0182	1
47DAP/reference	1.24387	0.133
52DAP/reference	1.81515	0.007
57DAP/reference	3.19744	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.35364	0.004
17DAP/reference	0.46155	0.003
27DAP/reference	0.68435	0.027
39DAP/reference	0.75695	0.034
41DAP/reference	1.17829	0.153
42DAP/reference	1.21643	0.094
43DAP/reference	0.89409	0.298
47DAP/reference	3.86492	0.008
52DAP/reference	1.32033	0.006
57DAP/reference	1.76733	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58678	0.028
17DAP/reference	0.61063	0.082
27DAP/reference	0.87024	0.23
39DAP/reference	1.37649	0.052
41DAP/reference	1.24951	0.033
42DAP/reference	1.274	0.111
43DAP/reference	1.35601	0.069
47DAP/reference	2.66471	0.005
52DAP/reference	2.55355	0.028
57DAP/reference	1.38107	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12024	0.966
26DAP/20DAP	1.1512	0.713
34DAP/26DAP	1.48089	0.542
51DAP/34DAP	3.31177	0.021
52DAP/51DAP	0.71595	0.151
53DAP/52DAP	1.68334	0.028
55DAP/53DAP	0.51681	0.022
57DAP/55DAP	0.87402	0.475
62DAP/57DAP	2.62211	0.003
68DAP/62DAP	0.98542	0.81
68DAP/14DAP	2.48295	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87137	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.03	0.036
Mature Green Tomato/Ripe Tomato	0.30318	0.017
Immature Eggplant/Mature Eggplant	54.6533	0.05
Ripe Pepper/Ripe Tomato	1.97103	1
Mature Eggplant/Ripe Tomato	0.45181	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87459	0.616
1-1-2/M82	1.42306	1
12-2/M82	1.08595	1
12-4/M82	1.17905	1
1-3/M82	4.04888	0.277
2-1-1/M82	0.97216	1
2-1/M82	1.11167	1
2-6/M82	1.2577	0.374
3-2/M82	1.01413	1
4-1-1/M82	2.02948	1
4-1/M82	1.53293	1
4-3-2/M82	2.26901	0.508
4-3/M82	1.0666	1
5-3/M82	0.51326	0.49
6-2/M82	0.68533
6-3/M82	1.17693	1
7-1/M82	0.95123	0.509
7-2/M82	2.36231	0.324
9-3-2/M82	2.11991	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00526
IL2-6/WTpooled	0.92678
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12097	1
IL12-4/WTpooled	1.23604	0.785
IL1-4/WTpooled	1.59011	1
WT/WTpooled	0.94339	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	1.47477	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91186	1
DC3000/delta hrp 6h	0.74992	0.95
DC3000/delta hrp 12h	1.40566	1
DC3000/delta hrp 24h	0.90379	0.464

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82685	0.629
DC3000 delta B/DC3000 delta AB	1.44408	0.234

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14767	1
Exp 36h	1.14266	1
Exp 60h	1.01894	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97855	1
Var 0h	0.93523	1
Var 12h I row2-row1	0.85578	0.514
Var 12h NI row2-row1	1.36092	0.649
Var 36h I row2-row1	1.09859	1
Var 36h NI row2-row1	0.78757	0.61
Var 60h I row2-row1	0.53564	0.285
Var 60h NI row2-row1	0.65738	0.306
Time course 0hI-0hNI	1.15074	0.377
Time course 12hI-12hNI	1.37617	0.113
Time course 36hI-36hNI	3.40533	0.005
Time course 60hI-60hNI	10.158	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)	0.55166	0.314
transgenic ySAMdc/azygous control (breaker)	1.02505	1
transgenic ySAMdc/azygous control (red)	1.12079	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.62827	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75046	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.05021	0.096
Manapal/WT (break)	4.85084	0.183
Manapal/WT (red)	1.4475	0.15