Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.15.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43532	0.015
27DAP/17DAP	1.06527	0.872
39DAP/27DAP	1.8759	0.038
41DAP/39DAP	0.88548	0.54
42DAP/41DAP	0.88961	1
43DAP/42DAP	1.24956	0.873
47DAP/43DAP	0.99701	0.868
52DAP/47DAP	1.45064	0.371
57DAP/52DAP	0.92317	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16822	0.097
17DAP/reference	1.04466	0.258
27DAP/reference	1.02316	0.709
39DAP/reference	0.95937	0.424
41DAP/reference	1.12861	0.013
42DAP/reference	0.90125	0.041
43DAP/reference	1.00977	1
47DAP/reference	0.94082	0.106
52DAP/reference	0.8715	0.099
57DAP/reference	0.9979	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.35113	0.025
27DAP/17DAP	1.07363	0.805
39DAP/27DAP	1.3427	0.08
41DAP/39DAP	1.04148	0.807
42DAP/41DAP	1.01573	0.816
43DAP/42DAP	1.81091	0.014
47DAP/43DAP	1.0976	0.529
52DAP/47DAP	1.41498	0.286
57DAP/52DAP	3.63904	0.03
57DAP/7DAP	1.34532	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98986	0.682
17DAP/reference	0.91999	0.22
27DAP/reference	1.10736	0.301
39DAP/reference	0.9388	0.17
41DAP/reference	0.95687	0.341
42DAP/reference	0.82997	0.077
43DAP/reference	0.80878	0.015
47DAP/reference	0.99387	1
52DAP/reference	0.76506	0.023
57DAP/reference	0.96112	0.411

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02312	0.842
17DAP/reference	0.91017	0.113
27DAP/reference	0.87334	0.09
39DAP/reference	0.88955	0.183
41DAP/reference	0.91683	0.156
42DAP/reference	0.88961	0.023
43DAP/reference	0.87759	0.087
47DAP/reference	0.99068	0.574
52DAP/reference	0.91086	0.047
57DAP/reference	1.02547	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92543	0.169
17DAP/reference	0.95248	0.508
27DAP/reference	0.84888	0.218
39DAP/reference	0.93466	0.222
41DAP/reference	0.93942	0.331
42DAP/reference	0.98323	0.671
43DAP/reference	0.88836	0.294
47DAP/reference	0.93058	0.306
52DAP/reference	0.84636	0.268
57DAP/reference	0.78442	0.037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87103	0.036
26DAP/20DAP	1.9437	0.555
34DAP/26DAP	0.83376	0.575
51DAP/34DAP	0.63144	0.061
52DAP/51DAP	1.61073	0.044
53DAP/52DAP	1.53774	0.034
55DAP/53DAP	1.00112	0.925
57DAP/55DAP	0.79049	0.238
62DAP/57DAP	1.47292	0.257
68DAP/62DAP	0.92703	0.722
68DAP/14DAP	0.94047	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.42629	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.16662	0.058
Mature Green Tomato/Ripe Tomato	0.7214	0.051
Immature Eggplant/Mature Eggplant	3.97492	0.05
Ripe Pepper/Ripe Tomato	0.2253	0.224
Mature Eggplant/Ripe Tomato	0.44332	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16181	0.591
1-1-2/M82	1.06549	1
12-2/M82	1.08779	1
12-4/M82	1.10166	1
1-3/M82	1.0772	1
2-1-1/M82	0.99329	1
2-1/M82	0.86756
2-6/M82	1.13276	0.505
3-2/M82	1.14553
4-1-1/M82	1.13153	1
4-1/M82	1.18397
4-3-2/M82	1.38467	0.241
4-3/M82	1.60999	0.268
5-3/M82	0.79306	0.642
6-2/M82	2.27008	0.212
6-3/M82	0.95994	1
7-1/M82	N/A	N/A
7-2/M82	1.35886	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.40957	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.3225	0.25
IL12-4/WTpooled	0.93858	1
IL1-4/WTpooled	0.96009	0.476
WT/WTpooled	1.14547	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	0.92846	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97018	1
DC3000/delta hrp 6h	0.89611	0.95
DC3000/delta hrp 12h	0.94506	1
DC3000/delta hrp 24h	1.91676	0.028

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01675	1
DC3000 delta B/DC3000 delta AB	1.15221	0.315

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93663	1
Exp 36h	1.1583	1
Exp 60h	0.9828	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98326	1
Var 0h	1.3129	0.216
Var 12h I row2-row1	1.25937	0.283
Var 12h NI row2-row1	0.92055	0.443
Var 36h I row2-row1	0.85758	0.805
Var 36h NI row2-row1	1.48847	1
Var 60h I row2-row1	0.74433	0.285
Var 60h NI row2-row1	1.58161	0.904
Time course 0hI-0hNI	1.03749	0.852
Time course 12hI-12hNI	1.03151	0.816
Time course 36hI-36hNI	0.93716	0.215
Time course 60hI-60hNI	1.34066	0.053

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)	1.25674	0.372
transgenic ySAMdc/azygous control (breaker)	0.77524	0.173
transgenic ySAMdc/azygous control (red)	1.19361	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.19	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90528	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02605	1
Manapal/WT (break)	1.00859	1
Manapal/WT (red)	0.86158	0.184