Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96335	0.419
27DAP/17DAP	1.07965	0.91
39DAP/27DAP	1.21369	0.782
41DAP/39DAP	0.93959	0.802
42DAP/41DAP	1.04859	0.994
43DAP/42DAP	1.92603	0.601
47DAP/43DAP	0.85188	0.533
52DAP/47DAP	1.3781	0.739
57DAP/52DAP	0.91869	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09609	0.252
17DAP/reference	0.9868	0.777
27DAP/reference	0.94658	0.525
39DAP/reference	0.8676	0.128
41DAP/reference	0.93368	0.542
42DAP/reference	1.0428	0.398
43DAP/reference	0.96051	0.538
47DAP/reference	0.91932	0.191
52DAP/reference	1.05109	0.167
57DAP/reference	0.99317	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28569	0.716
27DAP/17DAP	0.76464	0.748
39DAP/27DAP	0.49265	0.029
41DAP/39DAP	1.62838	0.19
42DAP/41DAP	0.94999	0.721
43DAP/42DAP	1.15572	0.664
47DAP/43DAP	1.15576	0.906
52DAP/47DAP	2.5112	0.133
57DAP/52DAP	2.38507	0.045
57DAP/7DAP	1.81095	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94583	0.445
17DAP/reference	1.07986	0.971
27DAP/reference	0.7524	0.019
39DAP/reference	0.90225	0.17
41DAP/reference	0.91317	0.094
42DAP/reference	0.97977	0.531
43DAP/reference	1.05354	0.167
47DAP/reference	0.80086	0.128
52DAP/reference	0.78776	0.04
57DAP/reference	1.19715	0.049

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9994	0.951
17DAP/reference	0.96457	0.499
27DAP/reference	1.03772	1
39DAP/reference	1.18326	0.272
41DAP/reference	1.04673	0.614
42DAP/reference	1.01989	1
43DAP/reference	1.09806	0.598
47DAP/reference	1.08181	0.467
52DAP/reference	1.03274	1
57DAP/reference	1.15085	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87612	0.169
17DAP/reference	0.94182	0.47
27DAP/reference	1.33421	0.967
39DAP/reference	0.98638	0.693
41DAP/reference	0.82825	0.096
42DAP/reference	0.92377	0.287
43DAP/reference	1.0072	0.767
47DAP/reference	0.93415	0.224
52DAP/reference	0.89027	0.464
57DAP/reference	1.17752	0.218

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88433	1
26DAP/20DAP	1.25922	0.604
34DAP/26DAP	1.42005	0.819
51DAP/34DAP	1.13135	0.84
52DAP/51DAP	1.17445
53DAP/52DAP	1.12551	0.608
55DAP/53DAP	0.93063	0.725
57DAP/55DAP	1.1028	0.87
62DAP/57DAP	0.81298	0.088
68DAP/62DAP	1.53194	0.013
68DAP/14DAP	0.89153	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76231	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.09364	0.017
Immature Eggplant/Mature Eggplant	0.25437
Ripe Pepper/Ripe Tomato	0.45429	0.224
Mature Eggplant/Ripe Tomato	0.68024	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96669
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.75777	0.277
IL2-6/WTpooled	0.96866	1
IL7-5/WTpooled	0.43855	1
IL7-3/WTpooled	1.08335	1
IL12-4/WTpooled	1.14926	0.839
IL1-4/WTpooled	0.85827	0.444
WT/WTpooled	1.15281	0.87

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	0.98125	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91676	0.868
DC3000/delta hrp 6h	1.47374	1
DC3000/delta hrp 12h	1.0909	1
DC3000/delta hrp 24h	0.88329	0.298

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13854	0.201
Exp 36h	N/A	N/A
Exp 60h	1.21709	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.87676
Var 0h	0.76292	0.933
Var 12h I row2-row1	1.30035	0.296
Var 12h NI row2-row1	1.28087	0.649
Var 36h I row2-row1	0.72612	0.805
Var 36h NI row2-row1	0.74885	1
Var 60h I row2-row1	0.70686	0.306
Var 60h NI row2-row1	0.74935	1
Time course 0hI-0hNI	1.34614	0.413
Time course 12hI-12hNI	2.89336	0.004
Time course 36hI-36hNI	1.9489	0.007
Time course 60hI-60hNI	2.40583	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)	1.42482	0.212
transgenic ySAMdc/azygous control (breaker)	0.52972	0.15
transgenic ySAMdc/azygous control (red)	0.89689	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00201	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66722	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6896	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A