Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.17.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04802	0.912
27DAP/17DAP	1.19116	0.8
39DAP/27DAP	0.99567	0.719
41DAP/39DAP	1.44956	0.185
42DAP/41DAP	0.89456	1
43DAP/42DAP	1.06429	1
47DAP/43DAP	0.95256	0.794
52DAP/47DAP	1.07205	0.869
57DAP/52DAP	1.04517	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08681	0.872
17DAP/reference	1.10451	0.492
27DAP/reference	1.44204	0.01
39DAP/reference	1.13695	0.153
41DAP/reference	1.11699	0.203
42DAP/reference	0.97205	0.315
43DAP/reference	0.97504	0.691
47DAP/reference	1.04073	1
52DAP/reference	1.23345	0.335
57DAP/reference	1.00573	0.767

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05168	0.605
27DAP/17DAP	0.98665	0.943
39DAP/27DAP	1.09315	0.541
41DAP/39DAP	1.03629	0.868
42DAP/41DAP	0.95748	0.679
43DAP/42DAP	1.06039	0.351
47DAP/43DAP	1.06587	0.485
52DAP/47DAP	1.0064	1
57DAP/52DAP	1.02144	0.917
57DAP/7DAP	1.02913	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92671	0.296
17DAP/reference	0.87086	0.072
27DAP/reference	1.02508	0.551
39DAP/reference	1.13405	0.059
41DAP/reference	1.03003	0.891
42DAP/reference	1.02892	0.686
43DAP/reference	1.07218	0.788
47DAP/reference	0.92381	0.383
52DAP/reference	0.9971	0.74
57DAP/reference	0.96896	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11227	0.75
17DAP/reference	1.17911	0.139
27DAP/reference	0.92084	0.34
39DAP/reference	1.05954	0.868
41DAP/reference	1.27314	0.099
42DAP/reference	1.05313	1
43DAP/reference	1.05975	1
47DAP/reference	0.88782	0.02
52DAP/reference	0.99393	0.619
57DAP/reference	1.22965	0.508

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91059	0.147
17DAP/reference	1.01823	1
27DAP/reference	0.82555	0.065
39DAP/reference	1.01912	0.962
41DAP/reference	1.01749	0.796
42DAP/reference	1.08772	0.923
43DAP/reference	1.09124	0.71
47DAP/reference	1.13956	0.901
52DAP/reference	0.87255	0.153
57DAP/reference	1.07186	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.62204	0.014
26DAP/20DAP	0.89899	0.512
34DAP/26DAP	1.02787	1
51DAP/34DAP	1.00074	0.96
52DAP/51DAP	1.06338	0.565
53DAP/52DAP	0.98263	0.917
55DAP/53DAP	1.10561	0.487
57DAP/55DAP	0.96231	0.851
62DAP/57DAP	1.10558	0.935
68DAP/62DAP	0.74356	0.579
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79632	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.99831	0.835
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.90612
12-2/M82	N/A	N/A
12-4/M82	0.78638
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	0.93933
4-1-1/M82	N/A	N/A
4-1/M82	0.84147	1
4-3-2/M82	0.84515	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	1.0153	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.33634	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.58573	0.31
IL12-4/WTpooled	0.83639	0.71
IL1-4/WTpooled	1.06268
WT/WTpooled	1.02727	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	0.85587	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20361	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.95739	1
DC3000/delta hrp 24h	2.04729

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64975	0.026
DC3000 delta B/DC3000 delta AB	0.56872	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
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	1.03914	1
Var 0h	1.904	0.782
Var 12h I row2-row1	0.9018	0.514
Var 12h NI row2-row1	0.55681	0.36
Var 36h I row2-row1	1.03257	1
Var 36h NI row2-row1	1.95868	0.482
Var 60h I row2-row1	1.56073	0.562
Var 60h NI row2-row1	1.56244	0.691
Time course 0hI-0hNI	0.74403	0.051
Time course 12hI-12hNI	1.12516	0.26
Time course 36hI-36hNI	1.01294	1
Time course 60hI-60hNI	0.11935	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	4.27643	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.50083	1
Manapal/WT (break)	1.50537	1
Manapal/WT (red)	1.70126	0.164