Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.3.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4826	0.138
27DAP/17DAP	0.90754	0.796
39DAP/27DAP	0.92626	0.67
41DAP/39DAP	0.64772	0.1
42DAP/41DAP	1.1227	0.933
43DAP/42DAP	1.21695	0.722
47DAP/43DAP	1.15292	0.555
52DAP/47DAP	0.55418	0.078
57DAP/52DAP	1.11811	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73185	0.024
17DAP/reference	0.86879	0.208
27DAP/reference	1.35654	0.394
39DAP/reference	1.58105	0.359
41DAP/reference	1.23133	0.855
42DAP/reference	0.94278	0.268
43DAP/reference	0.74835	0.222
47DAP/reference	0.87693	0.207
52DAP/reference	1.07295	0.354
57DAP/reference	1.71549	0.109

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.64069	0.036
27DAP/17DAP	0.7944	0.158
39DAP/27DAP	0.67972	0.028
41DAP/39DAP	1.13247	0.579
42DAP/41DAP	0.91302	0.453
43DAP/42DAP	0.83512	0.06
47DAP/43DAP	0.91823	0.373
52DAP/47DAP	1.03303	0.927
57DAP/52DAP	0.83996	0.047
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23678	0.11
17DAP/reference	1.5705	0.007
27DAP/reference	1.43779	0.011
39DAP/reference	1.52802	0.008
41DAP/reference	1.6092	0.011
42DAP/reference	1.58928	0.007
43DAP/reference	1.36787	0.007
47DAP/reference	1.43433	0.02
52DAP/reference	1.37804	0.029
57DAP/reference	1.30601	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79637	0.145
17DAP/reference	0.91081	0.317
27DAP/reference	0.99599	0.686
39DAP/reference	1.00096	0.702
41DAP/reference	1.06679	0.491
42DAP/reference	0.90642	0.042
43DAP/reference	0.8826	0.217
47DAP/reference	0.99745	0.714
52DAP/reference	1.01345	1
57DAP/reference	0.73615	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2671	0.146
17DAP/reference	1.32338	0.384
27DAP/reference	1.65578	0.024
39DAP/reference	1.47133	0.014
41DAP/reference	1.37783	0.011
42DAP/reference	1.24915	0.716
43DAP/reference	1.66372	0.007
47DAP/reference	1.56652	0.006
52DAP/reference	1.75988	0.066
57DAP/reference	1.49677	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18912	0.047
26DAP/20DAP	1.04922	1
34DAP/26DAP	0.88876	0.811
51DAP/34DAP	1.33555	0.089
52DAP/51DAP	0.78617	1
53DAP/52DAP	0.94108	0.783
55DAP/53DAP	0.96515	0.796
57DAP/55DAP	0.86516	0.568
62DAP/57DAP	1.07987	0.902
68DAP/62DAP	1.62609	0.178
68DAP/14DAP	3.03242	0.026

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.53101	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70377	0.188
Mature Green Tomato/Ripe Tomato	1.63519	0.022
Immature Eggplant/Mature Eggplant	0.9416	0.493
Ripe Pepper/Ripe Tomato	1.66836	1
Mature Eggplant/Ripe Tomato	1.19645	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16701	0.877
1-1-2/M82	1.51247
12-2/M82	0.8909	0.678
12-4/M82	1.20738	1
1-3/M82	1.39909	0.248
2-1-1/M82	0.786
2-1/M82	0.44587
2-6/M82	0.9876	1
3-2/M82	1.00454	1
4-1-1/M82	1.66358
4-1/M82	1.84393	0.853
4-3-2/M82	1.56636	1
4-3/M82	1.40676	0.268
5-3/M82	0.81818	0.642
6-2/M82	N/A	N/A
6-3/M82	0.48448
7-1/M82	0.77798	0.408
7-2/M82	0.97672	1
9-3-2/M82	2.02061	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00391	1
IL2-6/WTpooled	1.03775	1
IL7-5/WTpooled	1.30708	0.75
IL7-3/WTpooled	0.9566	1
IL12-4/WTpooled	1.03291	0.646
IL1-4/WTpooled	0.87321	0.699
WT/WTpooled	0.99278	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	1.08912	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95927	1
DC3000/delta hrp 6h	1.01968	1
DC3000/delta hrp 12h	1.04459	1
DC3000/delta hrp 24h	0.8868	0.346

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	0.83446	0.06

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00826	1
Exp 36h	0.75412	0.539
Exp 60h	0.82635	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98871	1
Var 0h	1.00605	1
Var 12h I row2-row1	1.01724	1
Var 12h NI row2-row1	1.12157	0.34
Var 36h I row2-row1	1.00576	1
Var 36h NI row2-row1	1.0678	0.482
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.97721	1
Time course 0hI-0hNI	0.99496	1
Time course 12hI-12hNI	0.9068	0.279
Time course 36hI-36hNI	0.89723	0.15
Time course 60hI-60hNI	0.29159	0.005

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)	0.98447	0.662
transgenic ySAMdc/azygous control (breaker)	1.28907	0.248
transgenic ySAMdc/azygous control (red)	1.16635	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98934	0.588

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43787	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.62386	0.086
Manapal/WT (break)	1.84515	0.14
Manapal/WT (red)	2.86327	0.133