Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.13.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0386	0.997
27DAP/17DAP	1.52371	0.683
39DAP/27DAP	1.03232	0.84
41DAP/39DAP	1.11695	0.56
42DAP/41DAP	1.18429	0.647
43DAP/42DAP	1.09436	1
47DAP/43DAP	1.02281	0.979
52DAP/47DAP	1.06037	0.964
57DAP/52DAP	1.11782	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90274	0.041
17DAP/reference	0.97161	0.298
27DAP/reference	0.96207	0.249
39DAP/reference	0.92099	0.247
41DAP/reference	0.9992	0.814
42DAP/reference	0.8613	0.003
43DAP/reference	0.95308	0.302
47DAP/reference	0.90459	0.005
52DAP/reference	0.9138	0.158
57DAP/reference	0.91573	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98648	0.763
27DAP/17DAP	1.02582	0.912
39DAP/27DAP	0.99764	1
41DAP/39DAP	1.05242	0.774
42DAP/41DAP	0.95573	0.61
43DAP/42DAP	0.95479	0.321
47DAP/43DAP	0.98896	0.933
52DAP/47DAP	1.04403	0.816
57DAP/52DAP	1.06212	0.627
57DAP/7DAP	1.10598	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90502	0.06
17DAP/reference	0.97837	0.338
27DAP/reference	0.9519	0.109
39DAP/reference	1.00776	0.865
41DAP/reference	0.97341	0.213
42DAP/reference	0.98924	0.582
43DAP/reference	0.87762	0.126
47DAP/reference	0.89315	0.222
52DAP/reference	0.9258	0.046
57DAP/reference	0.91302	0.083

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00771	0.979
17DAP/reference	0.94492	0.153
27DAP/reference	0.87628	0.111
39DAP/reference	0.89208	0.113
41DAP/reference	0.86647	0.076
42DAP/reference	0.96218	0.355
43DAP/reference	0.97243	0.569
47DAP/reference	1.01414	0.816
52DAP/reference	0.90588	0.031
57DAP/reference	1.05218	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95581	0.054
17DAP/reference	0.93954	0.55
27DAP/reference	0.98071	0.286
39DAP/reference	1.00622	1
41DAP/reference	0.91041	0.371
42DAP/reference	0.87199	0.287
43DAP/reference	0.85298	0.049
47DAP/reference	0.93953	0.24
52DAP/reference	1.01116	0.99
57DAP/reference	0.76438	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98597	1
26DAP/20DAP	0.94146	0.512
34DAP/26DAP	0.99169	1
51DAP/34DAP	1.07441	0.445
52DAP/51DAP	1.02988	0.708
53DAP/52DAP	0.93254	0.75
55DAP/53DAP	0.93823	0.761
57DAP/55DAP	1.12726	0.87
62DAP/57DAP	1.01345	1
68DAP/62DAP	0.93525	0.747
68DAP/14DAP	1.07329	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91355	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.00609	0.847
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.00769	1
Ripe Pepper/Ripe Tomato	0.81725	0.293
Mature Eggplant/Ripe Tomato	0.45153	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07309	0.742
1-1-2/M82	1.09673
12-2/M82	1.0741	1
12-4/M82	0.98165	1
1-3/M82	0.84839	0.441
2-1-1/M82	1.1216	0.764
2-1/M82	0.8533	1
2-6/M82	1.00392	1
3-2/M82	1.10305
4-1-1/M82	1.01398	1
4-1/M82	1.27576	0.853
4-3-2/M82	0.99591	1
4-3/M82	1.01889	1
5-3/M82	0.97175	1
6-2/M82	0.91595	0.497
6-3/M82	0.96215	1
7-1/M82	1.03693	1
7-2/M82	1.00872	1
9-3-2/M82	0.91806	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.95267	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86139	0.418
IL12-4/WTpooled	0.89818	0.71
IL1-4/WTpooled	0.92692	0.834
WT/WTpooled	0.94742	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	0.97987	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9665	1
DC3000/delta hrp 6h	1.311	1
DC3000/delta hrp 12h	0.92668	1
DC3000/delta hrp 24h	1.03747	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07838	0.063
DC3000 delta B/DC3000 delta AB	1.04598	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00452	1
Exp 36h	1.20837	1
Exp 60h	1.28126	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01902	1
Var 0h	0.8244	1
Var 12h I row2-row1	1.20769	0.228
Var 12h NI row2-row1	1.06315	0.281
Var 36h I row2-row1	0.93442	1
Var 36h NI row2-row1	0.84566	0.522
Var 60h I row2-row1	1.12903	1
Var 60h NI row2-row1	1.27183	0.904
Time course 0hI-0hNI	1.0807	0.852
Time course 12hI-12hNI	1.01081	1
Time course 36hI-36hNI	0.99752	0.798
Time course 60hI-60hNI	1.17721	0.019

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)	0.82961	0.213
transgenic ySAMdc/azygous control (breaker)	1.09385	0.248
transgenic ySAMdc/azygous control (red)	0.98166	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99315	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88946	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92487	1
Manapal/WT (break)	0.86961	1
Manapal/WT (red)	0.98927	0.863