Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63375	0.024
27DAP/17DAP	1.27723	0.801
39DAP/27DAP	1.08661	0.882
41DAP/39DAP	0.88595	0.543
42DAP/41DAP	0.75247	0.774
43DAP/42DAP	2.51019	0.127
47DAP/43DAP	0.68109	0.183
52DAP/47DAP	1.80292	0.48
57DAP/52DAP	0.78934	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90114	0.125
17DAP/reference	0.85685	0.097
27DAP/reference	1.11853	0.559
39DAP/reference	0.96614	0.68
41DAP/reference	0.83658	0.049
42DAP/reference	1.44822	0.001
43DAP/reference	1.03604	0.866
47DAP/reference	1.25662	0.093
52DAP/reference	1.51887	0.009
57DAP/reference	1.37974	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80998	0.126
27DAP/17DAP	1.13738	0.458
39DAP/27DAP	1.00667	1
41DAP/39DAP	0.89499	0.645
42DAP/41DAP	0.96672	0.712
43DAP/42DAP	0.97973	0.831
47DAP/43DAP	1.01672	0.956
52DAP/47DAP	0.97965	0.9
57DAP/52DAP	1.14343	0.424
57DAP/7DAP	0.65604	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2109	0.209
17DAP/reference	0.9451	0.338
27DAP/reference	1.00473	0.8
39DAP/reference	1.00277	0.64
41DAP/reference	0.90844	0.203
42DAP/reference	1.08598	0.686
43DAP/reference	0.98571	0.58
47DAP/reference	1.31072	0.062
52DAP/reference	0.74442	0.017
57DAP/reference	0.78423	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80503	0.134
17DAP/reference	0.94915	0.143
27DAP/reference	0.91539	0.24
39DAP/reference	0.81352	0.024
41DAP/reference	0.83777	0.013
42DAP/reference	0.94418	0.261
43DAP/reference	0.79794	0.082
47DAP/reference	0.94748	0.311
52DAP/reference	0.79918	0.031
57DAP/reference	0.75923	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07583	0.481
17DAP/reference	0.78911	0.078
27DAP/reference	0.86811	0.165
39DAP/reference	0.81932	0.024
41DAP/reference	0.89998	0.185
42DAP/reference	1.03404	1
43DAP/reference	0.81914	0.267
47DAP/reference	1.09181	0.562
52DAP/reference	1.87151	0.146
57DAP/reference	1.07608	0.636

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.38972	0.945
26DAP/20DAP	1.87348	0.099
34DAP/26DAP	0.85813	0.162
51DAP/34DAP	1.0368	0.84
52DAP/51DAP	1.24576	0.176
53DAP/52DAP	0.75009	0.101
55DAP/53DAP	0.77979	0.13
57DAP/55DAP	1.1478	0.745
62DAP/57DAP	1.32879	0.185
68DAP/62DAP	1.33914	0.155
68DAP/14DAP	2.58231	0.077

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.91384	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05476	0.287
Mature Green Tomato/Ripe Tomato	0.71095	0.06
Immature Eggplant/Mature Eggplant	0.67943	0.062
Ripe Pepper/Ripe Tomato	0.59154	0.224
Mature Eggplant/Ripe Tomato	0.55588	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.4439	0.591
1-1-2/M82	1.17967	0.891
12-2/M82	0.92759
12-4/M82	1.05551	0.694
1-3/M82	1.4792	0.248
2-1-1/M82	1.17593	0.179
2-1/M82	1.24166
2-6/M82	1.1589	0.425
3-2/M82	1.0959
4-1-1/M82	1.05866	1
4-1/M82	0.47222
4-3-2/M82	0.90306
4-3/M82	1.00513	1
5-3/M82	1.08703	0.572
6-2/M82	0.75253
6-3/M82	1.10083	1
7-1/M82	0.90268	1
7-2/M82	1.28003	0.324
9-3-2/M82	0.97521

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31672	0.277
IL2-6/WTpooled	0.81084	0.358
IL7-5/WTpooled	1.1961	0.75
IL7-3/WTpooled	0.96547	0.418
IL12-4/WTpooled	0.93148	0.581
IL1-4/WTpooled	0.92579	0.699
WT/WTpooled	1.03264	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	1.13041	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04806	0.921
DC3000/delta hrp 6h	1.06996	1
DC3000/delta hrp 12h	0.86245	1
DC3000/delta hrp 24h	1.13612	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25317	0.063
DC3000 delta B/DC3000 delta AB	1.47932	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80588	1
Exp 36h	1.01538	1
Exp 60h	1.06979	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00744	1
Var 0h	1.59567	0.782
Var 12h I row2-row1	0.93642	0.565
Var 12h NI row2-row1	1.16409	0.649
Var 36h I row2-row1	1.04472	1
Var 36h NI row2-row1	0.83479	0.478
Var 60h I row2-row1	0.84278	0.582
Var 60h NI row2-row1	0.84526	0.69
Time course 0hI-0hNI	1.09746	0.662
Time course 12hI-12hNI	1.01175	0.885
Time course 36hI-36hNI	1.35023	0.006
Time course 60hI-60hNI	1.55284	0.009

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)	0.92873	0.348
transgenic ySAMdc/azygous control (breaker)	2.10386	0.172
transgenic ySAMdc/azygous control (red)	0.97553	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02596	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.55224	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.55279	0.14
Manapal/WT (break)	0.94903	1
Manapal/WT (red)	0.99624	1