Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.6.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70012	0.173
27DAP/17DAP	1.37792	0.752
39DAP/27DAP	1.26721	0.762
41DAP/39DAP	0.69285	0.147
42DAP/41DAP	1.2869	0.797
43DAP/42DAP	0.9908	0.937
47DAP/43DAP	0.69992	0.127
52DAP/47DAP	1.95076	0.12
57DAP/52DAP	0.78016	0.711

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87313	0.188
17DAP/reference	0.91179	0.24
27DAP/reference	0.98966	0.779
39DAP/reference	0.95493	0.565
41DAP/reference	0.85673	0.014
42DAP/reference	0.98522	0.425
43DAP/reference	1.02531	0.838
47DAP/reference	0.92353	0.148
52DAP/reference	1.02506	1
57DAP/reference	1.13386	0.366

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91962	0.542
27DAP/17DAP	0.84109	0.446
39DAP/27DAP	1.40666	0.078
41DAP/39DAP	2.13671	0.025
42DAP/41DAP	1.51224	0.674
43DAP/42DAP	1.20693	0.042
47DAP/43DAP	1.26835	0.09
52DAP/47DAP	1.36955	0.356
57DAP/52DAP	1.64099	0.139
57DAP/7DAP	1.09569

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81612	0.082
17DAP/reference	1.14327	0.477
27DAP/reference	0.91448	0.071
39DAP/reference	1.10237	0.486
41DAP/reference	1.04262	0.701
42DAP/reference	1.17842	0.686
43DAP/reference	1.73155	0.007
47DAP/reference	1.03186	0.948
52DAP/reference	1.63457	0.017
57DAP/reference	2.18271	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90829	0.222
17DAP/reference	0.80616	0.009
27DAP/reference	0.84129	0.017
39DAP/reference	1.0652	1
41DAP/reference	0.99211	0.531
42DAP/reference	0.88992	0.189
43DAP/reference	1.04658	1
47DAP/reference	0.96626	0.4
52DAP/reference	1.00143	0.666
57DAP/reference	0.99179	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85026	0.049
17DAP/reference	1.01515	1
27DAP/reference	1.0723	0.487
39DAP/reference	1.15359	0.182
41DAP/reference	1.02743	0.84
42DAP/reference	0.96201	0.552
43DAP/reference	1.06658	0.815
47DAP/reference	1.01109	0.731
52DAP/reference	1.0601	0.631
57DAP/reference	0.93523	0.253

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16075	0.966
26DAP/20DAP	0.83298	0.317
34DAP/26DAP	1.09399	1
51DAP/34DAP	0.54151	0.22
52DAP/51DAP	1.52588	0.193
53DAP/52DAP	0.86972	0.604
55DAP/53DAP	1.15888	0.689
57DAP/55DAP	1.00679	1
62DAP/57DAP	1.13549	0.833
68DAP/62DAP	1.27863	0.991
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.85898	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.20863
Mature Green Tomato/Ripe Tomato	0.22875	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.22338	1
Mature Eggplant/Ripe Tomato	0.31325	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98894	1
1-1-2/M82	0.87724	1
12-2/M82	2.45831	0.306
12-4/M82	0.89537	0.619
1-3/M82	0.81693	0.378
2-1-1/M82	0.71429	0.465
2-1/M82	0.76763	0.322
2-6/M82	0.98749	1
3-2/M82	1.28915	0.717
4-1-1/M82	1.09736	1
4-1/M82	1.3489	0.512
4-3-2/M82	0.77462	0.487
4-3/M82	0.61945	0.72
5-3/M82	0.72389	0.642
6-2/M82	1.1703	1
6-3/M82	0.87102
7-1/M82	0.7878	0.803
7-2/M82	N/A	N/A
9-3-2/M82	0.69972	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93892	1
IL2-6/WTpooled	0.75031	0.383
IL7-5/WTpooled	1.04095	1
IL7-3/WTpooled	1.10369	1
IL12-4/WTpooled	0.70281	0.484
IL1-4/WTpooled	0.96517	0.834
WT/WTpooled	0.97814	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	1.04139	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10958	0.656
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.97185	1
DC3000/delta hrp 24h	1.10805	0.347

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44048	0.042
DC3000 delta B/DC3000 delta AB	1.12867	0.42

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	1.03723	1
Var 0h	0.7376	0.933
Var 12h I row2-row1	1.14297	0.211
Var 12h NI row2-row1	0.46522	0.713
Var 36h I row2-row1	1.14273	0.601
Var 36h NI row2-row1	1.22757	1
Var 60h I row2-row1	0.90539	0.582
Var 60h NI row2-row1	0.98781	1
Time course 0hI-0hNI	1.09877	0.603
Time course 12hI-12hNI	1.22245	0.083
Time course 36hI-36hNI	1.8693	0.005
Time course 60hI-60hNI	1.91908	0.008

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)	0.87061	0.237
transgenic ySAMdc/azygous control (breaker)	1.2515	0.248
transgenic ySAMdc/azygous control (red)	1.14528	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07316	0.071

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81857	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18767	1
Manapal/WT (break)	1.61565	0.381
Manapal/WT (red)	0.83097	0.424