Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.15.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.85701	0.23
27DAP/17DAP	0.70254	0.209
39DAP/27DAP	0.7935	0.474
41DAP/39DAP	1.12034	0.982
42DAP/41DAP	1.11115	0.92
43DAP/42DAP	0.83124	0.754
47DAP/43DAP	2.01667	0.246
52DAP/47DAP	1.48174	0.48
57DAP/52DAP	0.95404	0.938

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99756	0.743
17DAP/reference	0.93861	0.474
27DAP/reference	0.93749	0.275
39DAP/reference	0.87752	0.076
41DAP/reference	1.02817	0.667
42DAP/reference	0.85117	0.006
43DAP/reference	0.99246	0.84
47DAP/reference	1.19152	0.012
52DAP/reference	1.66173	0.009
57DAP/reference	1.05087	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88587	0.363
27DAP/17DAP	1.22898	0.471
39DAP/27DAP	1.08908	0.742
41DAP/39DAP	0.90329	0.512
42DAP/41DAP	0.85492	0.109
43DAP/42DAP	1.04935	0.664
47DAP/43DAP	1.14687	0.529
52DAP/47DAP	1.08123	0.8
57DAP/52DAP	0.81146	0.188
57DAP/7DAP	0.86984	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.46351	0.076
17DAP/reference	1.70523	0.006
27DAP/reference	1.62884	0.007
39DAP/reference	1.78075	0.005
41DAP/reference	1.88824	0.012
42DAP/reference	1.99271	0.006
43DAP/reference	2.06991	0.007
47DAP/reference	1.23277	0.885
52DAP/reference	1.93777	0.007
57DAP/reference	1.47904	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0674	0.612
17DAP/reference	1.17945	0.136
27DAP/reference	0.84289	0.012
39DAP/reference	1.10163	0.263
41DAP/reference	0.87574	0.096
42DAP/reference	0.94669	0.237
43DAP/reference	0.91469	0.352
47DAP/reference	0.89911	0.126
52DAP/reference	0.91559	0.086
57DAP/reference	0.9275	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41646	0.015
17DAP/reference	1.13637	0.738
27DAP/reference	1.37906	0.065
39DAP/reference	1.51736	0.018
41DAP/reference	1.43535	0.01
42DAP/reference	1.44592	0.057
43DAP/reference	1.33139	0.214
47DAP/reference	0.91256	0.224
52DAP/reference	1.72226	0.077
57DAP/reference	1.32044	0.204

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07958	0.966
26DAP/20DAP	1.14362	0.642
34DAP/26DAP	1.06189	1
51DAP/34DAP	0.9628	0.77
52DAP/51DAP	0.98672	1
53DAP/52DAP	1.09142	0.688
55DAP/53DAP	1.16226	0.991
57DAP/55DAP	0.92307	0.688
62DAP/57DAP	1.22356	0.868
68DAP/62DAP	1.11219	0.944
68DAP/14DAP	0.86282	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05147	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.4219	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.17568	0.293
Mature Eggplant/Ripe Tomato	0.03587	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22736
1-1-2/M82	0.97507	1
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	0.8609	0.74
2-6/M82	1.09158	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.76378
4-1/M82	0.98228
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.68267
6-2/M82	N/A	N/A
6-3/M82	0.98695	1
7-1/M82	N/A	N/A
7-2/M82	1.03668
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75626	0.321
IL2-6/WTpooled	1.27502	0.584
IL7-5/WTpooled	1.03954	1
IL7-3/WTpooled	0.90263	0.294
IL12-4/WTpooled	0.91382	0.71
IL1-4/WTpooled	0.88783	0.476
WT/WTpooled	0.97334	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	0.85359	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97949	1
DC3000/delta hrp 6h	1.04691	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.12517	0.356

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	0.75002

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89142	1
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	1.00517
Var 0h	1.04466	1
Var 12h I row2-row1	0.63047	0.705
Var 12h NI row2-row1	0.81713	0.546
Var 36h I row2-row1	0.91189
Var 36h NI row2-row1	1.27376
Var 60h I row2-row1	0.8635
Var 60h NI row2-row1	0.73246	1
Time course 0hI-0hNI	1.05189	0.852
Time course 12hI-12hNI	0.97578	0.87
Time course 36hI-36hNI	0.92871	0.403
Time course 60hI-60hNI	0.81949	0.081

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)	1.20063	0.272
transgenic ySAMdc/azygous control (breaker)	0.94273	1
transgenic ySAMdc/azygous control (red)	1.05	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01169	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6831	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89449	1
Manapal/WT (break)	2.48933	0.14
Manapal/WT (red)	1.92405	0.222