Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.10.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47835	0.045
27DAP/17DAP	1.48167	0.413
39DAP/27DAP	0.96734	0.682
41DAP/39DAP	0.65619	0.082
42DAP/41DAP	0.74866	0.774
43DAP/42DAP	0.78403	0.524
47DAP/43DAP	0.80458	0.41
52DAP/47DAP	1.17732	0.786
57DAP/52DAP	0.91149	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85537	0.058
17DAP/reference	1.13052	0.33
27DAP/reference	1.17782	0.227
39DAP/reference	1.29115	0.061
41DAP/reference	1.36001	0.013
42DAP/reference	1.01547	0.517
43DAP/reference	0.98067	0.763
47DAP/reference	0.95174	0.258
52DAP/reference	0.90964	0.183
57DAP/reference	1.03113	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08348	0.438
27DAP/17DAP	0.87058	0.537
39DAP/27DAP	1.06607	0.691
41DAP/39DAP	0.85889	0.154
42DAP/41DAP	0.95924	0.69
43DAP/42DAP	0.62714	0.022
47DAP/43DAP	1.02178	0.99
52DAP/47DAP	1.0858	0.831
57DAP/52DAP	0.86109	0.264
57DAP/7DAP	0.91088	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84189	0.168
17DAP/reference	0.86408	0.035
27DAP/reference	1.0733	0.301
39DAP/reference	0.89896	0.073
41DAP/reference	1.04917	0.723
42DAP/reference	0.97967	0.482
43DAP/reference	0.80162	0.044
47DAP/reference	0.894	0.079
52DAP/reference	0.80415	0.021
57DAP/reference	0.80979	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26254	0.254
17DAP/reference	1.23891	0.081
27DAP/reference	1.52983	0.09
39DAP/reference	1.45943	0.042
41DAP/reference	1.3833	0.099
42DAP/reference	1.36375	0.021
43DAP/reference	2.27865	0.01
47DAP/reference	1.55578	0.009
52DAP/reference	1.29721	0.124
57DAP/reference	1.19753	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83593	0.112
17DAP/reference	1.11545	0.398
27DAP/reference	0.9994	0.843
39DAP/reference	1.0555	0.633
41DAP/reference	1.16767	0.502
42DAP/reference	1.05554	0.716
43DAP/reference	0.84953	0.106
47DAP/reference	1.00532	0.708
52DAP/reference	0.8247	0.15
57DAP/reference	1.23727	0.214

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11081	0.966
26DAP/20DAP	1.38642	0.683
34DAP/26DAP	0.88865	0.803
51DAP/34DAP	4.42341	0.032
52DAP/51DAP	1.14336	0.225
53DAP/52DAP	2.79668	0.02
55DAP/53DAP	1.57382	0.039
57DAP/55DAP	0.56725	0.03
62DAP/57DAP	0.38077	0.002
68DAP/62DAP	1.12803	0.926
68DAP/14DAP	1.73782	0.049

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.2194	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.14348	0.051
Mature Green Tomato/Ripe Tomato	10.4097	0.025
Immature Eggplant/Mature Eggplant	1.76803	0.05
Ripe Pepper/Ripe Tomato	17.8968	0.244
Mature Eggplant/Ripe Tomato	4.54602	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21673	0.877
1-1-2/M82	1.08479	1
12-2/M82	1.56626	0.448
12-4/M82	0.78868	1
1-3/M82	0.99797	1
2-1-1/M82	0.76464
2-1/M82	N/A	N/A
2-6/M82	0.89211	1
3-2/M82	0.85332	1
4-1-1/M82	0.89827	1
4-1/M82	1.90573
4-3-2/M82	0.72041	0.698
4-3/M82	0.76612	0.611
5-3/M82	1.02816	1
6-2/M82	0.66168	1
6-3/M82	1.0341	1
7-1/M82	1.04802	1
7-2/M82	0.94262	1
9-3-2/M82	0.76525

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89261	1
IL2-6/WTpooled	1.32793	0.46
IL7-5/WTpooled	1.19101	1
IL7-3/WTpooled	0.94054	0.418
IL12-4/WTpooled	0.87969	0.71
IL1-4/WTpooled	1.06742	1
WT/WTpooled	0.94157	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	1.14152	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08368	0.875
DC3000/delta hrp 6h	1.05922	1
DC3000/delta hrp 12h	0.95157	1
DC3000/delta hrp 24h	0.88453	0.166

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.94382	0.724
DC3000 delta B/DC3000 delta AB	1.2782	0.212

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07973	1
Exp 36h	0.99792	1
Exp 60h	1.26476	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04683	1
Var 0h	1.0531	1
Var 12h I row2-row1	0.9303	0.565
Var 12h NI row2-row1	1.06481	0.649
Var 36h I row2-row1	0.92622	1
Var 36h NI row2-row1	0.99903	1
Var 60h I row2-row1	0.78091	0.306
Var 60h NI row2-row1	0.98564	1
Time course 0hI-0hNI	1.02896	0.852
Time course 12hI-12hNI	0.99736	1
Time course 36hI-36hNI	1.08542	0.147
Time course 60hI-60hNI	1.22623	0.069

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)	1.03851	0.397
transgenic ySAMdc/azygous control (breaker)	0.71745	0.15
transgenic ySAMdc/azygous control (red)	1.0271	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07777	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43289	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83672	0.172
Manapal/WT (break)	0.83254	1
Manapal/WT (red)	1.48501	0.413