Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75535	0.331
27DAP/17DAP	2.97148	0.622
39DAP/27DAP	1.31991	0.774
41DAP/39DAP	1.08732	0.638
42DAP/41DAP	1.02364	1
43DAP/42DAP	1.23549	0.968
47DAP/43DAP	0.92484	0.671
52DAP/47DAP	1.34645	0.601
57DAP/52DAP	1.53225	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88255	0.073
17DAP/reference	0.89475	0.085
27DAP/reference	0.89627	0.134
39DAP/reference	0.84582	0.11
41DAP/reference	0.89975	0.341
42DAP/reference	0.8473	0.003
43DAP/reference	0.91434	0.093
47DAP/reference	0.92921	0.077
52DAP/reference	1.00112	0.768
57DAP/reference	0.98867	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16951	1
27DAP/17DAP	0.90698	0.537
39DAP/27DAP	1.05836	0.87
41DAP/39DAP	1.36282	0.735
42DAP/41DAP	0.69781	0.047
43DAP/42DAP	1.12227	0.699
47DAP/43DAP	0.96318	0.843
52DAP/47DAP	2.0712	0.16
57DAP/52DAP	3.33197	0.029
57DAP/7DAP	2.42506	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1443	0.292
17DAP/reference	0.96468	0.447
27DAP/reference	0.90094	0.018
39DAP/reference	0.73016	0.027
41DAP/reference	0.78582	0.054
42DAP/reference	0.7917	0.058
43DAP/reference	1.0281	0.764
47DAP/reference	0.83961	0.101
52DAP/reference	0.73656	0.028
57DAP/reference	1.1887	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05178	0.732
17DAP/reference	0.8149	0.02
27DAP/reference	0.83195	0.111
39DAP/reference	0.94633	0.322
41DAP/reference	0.90551	0.127
42DAP/reference	0.84665	0.05
43DAP/reference	0.84327	0.132
47DAP/reference	0.77237	0.011
52DAP/reference	0.90014	0.051
57DAP/reference	0.87326	0.023

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75066	0.059
17DAP/reference	0.72537	0.021
27DAP/reference	0.79129	0.04
39DAP/reference	0.78436	0.04
41DAP/reference	0.72448	0.031
42DAP/reference	0.84807	0.172
43DAP/reference	0.83613	0.073
47DAP/reference	0.936	0.278
52DAP/reference	1.63603	0.128
57DAP/reference	1.09495	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83737	0.807
26DAP/20DAP	0.80836	1
34DAP/26DAP	1.50216	0.819
51DAP/34DAP	2.53707	0.215
52DAP/51DAP	1.22344	0.626
53DAP/52DAP	1.17743	0.723
55DAP/53DAP	0.8911	0.577
57DAP/55DAP	0.90697	0.691
62DAP/57DAP	1.01585	1
68DAP/62DAP	1.15769	0.827
68DAP/14DAP	1.07352	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60801	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.85194	0.418
Mature Green Tomato/Ripe Tomato	1.19002	0.948
Immature Eggplant/Mature Eggplant	1.22556
Ripe Pepper/Ripe Tomato	0.44096	0.293
Mature Eggplant/Ripe Tomato	0.85023	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.74854
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	0.97618
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	0.90847	0.321
IL2-6/WTpooled	1.37328	0.531
IL7-5/WTpooled	0.86407	1
IL7-3/WTpooled	0.98263	1
IL12-4/WTpooled	0.89298	0.71
IL1-4/WTpooled	0.92101	0.562
WT/WTpooled	1.07614	0.999

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	0.72107

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95634	1
DC3000/delta hrp 6h	0.95093	0.95
DC3000/delta hrp 12h	1.205	1
DC3000/delta hrp 24h	1.06798	0.595

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.30329
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	0.92351	1
Exp 36h	1.03565	1
Exp 60h	0.93298	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.88777
Var 0h	N/A	N/A
Var 12h I row2-row1	1.85788	0.544
Var 12h NI row2-row1	2.45045	0.649
Var 36h I row2-row1	1.49762	0.368
Var 36h NI row2-row1	0.74256	0.743
Var 60h I row2-row1	0.79499	0.582
Var 60h NI row2-row1	1.02622	1
Time course 0hI-0hNI	0.8981	0.443
Time course 12hI-12hNI	1.13354	0.615
Time course 36hI-36hNI	1.33083	0.08
Time course 60hI-60hNI	1.61561	0.033

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)	1.57498	0.339
transgenic ySAMdc/azygous control (breaker)	0.64531	0.173
transgenic ySAMdc/azygous control (red)	1.60363	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10405	0.096

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84217	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80354	1
Manapal/WT (break)	1.01773	1
Manapal/WT (red)	0.85072	0.181