Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16002	0.863
27DAP/17DAP	0.92794	0.892
39DAP/27DAP	0.7739	0.399
41DAP/39DAP	1.39438	0.328
42DAP/41DAP	1.2823	0.709
43DAP/42DAP	0.97969	0.925
47DAP/43DAP	0.99873	0.934
52DAP/47DAP	1.21263	0.596
57DAP/52DAP	0.96572	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0558	0.147
17DAP/reference	1.074	0.086
27DAP/reference	0.9639	0.428
39DAP/reference	0.93036	0.114
41DAP/reference	1.05278	0.338
42DAP/reference	1.01298	0.995
43DAP/reference	0.98562	0.745
47DAP/reference	0.9258	0.106
52DAP/reference	1.02427	0.912
57DAP/reference	0.89478	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03149	0.762
27DAP/17DAP	0.96348	0.887
39DAP/27DAP	0.96536	0.682
41DAP/39DAP	1.05495	0.883
42DAP/41DAP	0.93139	0.412
43DAP/42DAP	1.03799	0.627
47DAP/43DAP	1.00082	1
52DAP/47DAP	0.9897	0.93
57DAP/52DAP	0.97204	0.716
57DAP/7DAP	1.24956	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85777	0.104
17DAP/reference	0.98293	0.447
27DAP/reference	0.93316	0.026
39DAP/reference	0.89871	0.013
41DAP/reference	0.76826	0.023
42DAP/reference	0.60348	0.01
43DAP/reference	0.7712	0.018
47DAP/reference	0.84855	0.222
52DAP/reference	0.8091	0.097
57DAP/reference	0.78289	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05546	0.33
17DAP/reference	1.21148	0.024
27DAP/reference	1.00765	1
39DAP/reference	1.18034	0.03
41DAP/reference	1.16887	0.318
42DAP/reference	1.01509	0.723
43DAP/reference	1.11565	0.242
47DAP/reference	0.92692	0.092
52DAP/reference	1.02353	0.761
57DAP/reference	1.11325	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99252	0.653
17DAP/reference	1.15532	0.182
27DAP/reference	0.85837	0.055
39DAP/reference	0.86662	0.092
41DAP/reference	0.96281	0.417
42DAP/reference	0.99712	1
43DAP/reference	0.97934	0.523
47DAP/reference	0.94992	0.249
52DAP/reference	1.22032	0.851
57DAP/reference	0.96595	0.491

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22029	0.586
26DAP/20DAP	0.8612	0.244
34DAP/26DAP	1.05866	0.542
51DAP/34DAP	0.93626	0.498
52DAP/51DAP	1.04678	0.606
53DAP/52DAP	0.94333	0.695
55DAP/53DAP	1.0765	0.562
57DAP/55DAP	0.9704	0.845
62DAP/57DAP	1.23144	0.081
68DAP/62DAP	0.92797	0.668
68DAP/14DAP	1.12252	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81007	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74753	0.212
Mature Green Tomato/Ripe Tomato	0.85967	0.411
Immature Eggplant/Mature Eggplant	0.77816	0.197
Ripe Pepper/Ripe Tomato	1.94916	0.258
Mature Eggplant/Ripe Tomato	2.3261	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90233	0.69
1-1-2/M82	0.9058	1
12-2/M82	0.93828	0.955
12-4/M82	0.98943	1
1-3/M82	0.86609	1
2-1-1/M82	1.2904
2-1/M82	0.98534
2-6/M82	1.08104	0.695
3-2/M82	N/A	N/A
4-1-1/M82	0.95384	1
4-1/M82	1.04506
4-3-2/M82	0.52112
4-3/M82	0.76539
5-3/M82	0.97722	1
6-2/M82	0.90163	0.497
6-3/M82	1.28304	1
7-1/M82	1.09728
7-2/M82	0.97898	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00619	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.07852	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.49948	0.581
IL1-4/WTpooled	1.07094	0.426
WT/WTpooled	2.17642	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	1.13491	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04544	0.921
DC3000/delta hrp 6h	1.01737	1
DC3000/delta hrp 12h	1.01303	1
DC3000/delta hrp 24h	0.97677	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13695	0.598
DC3000 delta B/DC3000 delta AB	0.93594	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.80425	0.265
Exp 36h	0.68709	0.406
Exp 60h	0.69441	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98705	1
Var 0h	0.97989	1
Var 12h I row2-row1	1.04556	0.692
Var 12h NI row2-row1	1.01243	1
Var 36h I row2-row1	0.86436	0.438
Var 36h NI row2-row1	1.50131	1
Var 60h I row2-row1	1.19259	0.543
Var 60h NI row2-row1	1.36971	0.904
Time course 0hI-0hNI	1.09444	0.799
Time course 12hI-12hNI	0.95646	0.701
Time course 36hI-36hNI	1.0424	0.874
Time course 60hI-60hNI	0.64752	0.015

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)	1.0822	0.384
transgenic ySAMdc/azygous control (breaker)	1.53757	0.172
transgenic ySAMdc/azygous control (red)	1.08859	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04916	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42948	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.65937	0.083
Manapal/WT (break)	1.73461	0.183
Manapal/WT (red)	0.84968	0.503