Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.10.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81953	0.173
27DAP/17DAP	1.01247	1
39DAP/27DAP	1.20213	0.796
41DAP/39DAP	1.41675	0.459
42DAP/41DAP	1.06736	1
43DAP/42DAP	0.88333	0.801
47DAP/43DAP	0.89693	0.58
52DAP/47DAP	1.42743	0.731
57DAP/52DAP	0.72974	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00829	1
17DAP/reference	0.99588	0.858
27DAP/reference	0.9459	0.538
39DAP/reference	0.89424	0.188
41DAP/reference	1.06473	0.171
42DAP/reference	1.00589	0.755
43DAP/reference	1.10348	0.118
47DAP/reference	0.98445	0.503
52DAP/reference	0.99904	0.709
57DAP/reference	1.02886	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10963	0.348
27DAP/17DAP	0.97721	0.919
39DAP/27DAP	0.95309	0.784
41DAP/39DAP	0.92129	0.63
42DAP/41DAP	1.02804	0.935
43DAP/42DAP	0.89521	0.224
47DAP/43DAP	1.05752	0.914
52DAP/47DAP	1.10913	0.696
57DAP/52DAP	0.98878	0.81
57DAP/7DAP	1.09834	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28262	0.039
17DAP/reference	0.98591	0.518
27DAP/reference	1.05943	0.06
39DAP/reference	1.22906	0.019
41DAP/reference	1.2626	0.057
42DAP/reference	1.36222	0.021
43DAP/reference	1.34805	0.01
47DAP/reference	1.65221	0.032
52DAP/reference	1.41079	0.031
57DAP/reference	1.13572	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09607	0.559
17DAP/reference	1.13041	0.448
27DAP/reference	1.13903	0.163
39DAP/reference	1.05399	0.746
41DAP/reference	1.06207	0.799
42DAP/reference	1.00254	0.723
43DAP/reference	1.03676	0.949
47DAP/reference	1.02094	0.994
52DAP/reference	0.88904	0.012
57DAP/reference	1.00058	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10855	0.422
17DAP/reference	0.89303	0.224
27DAP/reference	0.9835	0.539
39DAP/reference	1.33007	0.026
41DAP/reference	0.98725	0.682
42DAP/reference	1.16298	0.251
43DAP/reference	1.07384	0.867
47DAP/reference	0.90398	0.08
52DAP/reference	1.34744	0.09
57DAP/reference	1.53217	0.549

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01499	0.966
26DAP/20DAP	1.22174	0.305
34DAP/26DAP	1.03736	1
51DAP/34DAP	1.48763	0.177
52DAP/51DAP	1.03208	0.808
53DAP/52DAP	1.17406	0.537
55DAP/53DAP	0.99865	0.951
57DAP/55DAP	0.82823	0.36
62DAP/57DAP	0.85655	0.681
68DAP/62DAP	0.93454	0.641
68DAP/14DAP	1.32171	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13566	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80635	0.26
Mature Green Tomato/Ripe Tomato	1.47633	0.898
Immature Eggplant/Mature Eggplant	1.49916	0.052
Ripe Pepper/Ripe Tomato	1.78915	0.256
Mature Eggplant/Ripe Tomato	1.296	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86744	0.934
1-1-2/M82	0.95114
12-2/M82	1.12315	1
12-4/M82	0.68322	0.298
1-3/M82	1.12081	1
2-1-1/M82	0.9061	0.784
2-1/M82	1.02834
2-6/M82	0.85027	1
3-2/M82	0.69632
4-1-1/M82	0.74677	1
4-1/M82	1.34468
4-3-2/M82	0.96118	1
4-3/M82	1.20804	1
5-3/M82	1.05646	1
6-2/M82	0.85078
6-3/M82	1.05888	1
7-1/M82	0.82213
7-2/M82	0.97713	1
9-3-2/M82	0.84943	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.09747
IL2-6/WTpooled	1.2284	0.46
IL7-5/WTpooled	1.77301
IL7-3/WTpooled	0.57198	0.31
IL12-4/WTpooled	0.89561	0.71
IL1-4/WTpooled	0.88773	0.476
WT/WTpooled	1.08432	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	1.01736	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05442	0.894
DC3000/delta hrp 6h	1.15598	0.978
DC3000/delta hrp 12h	1.15506	1
DC3000/delta hrp 24h	0.93867	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97377	1
DC3000 delta B/DC3000 delta AB	1.11853	0.345

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.21819	1
Exp 36h	1.05405	1
Exp 60h	1.10201	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97727	1
Var 0h	1.17179	0.936
Var 12h I row2-row1	1.06606	0.544
Var 12h NI row2-row1	1.02914	1
Var 36h I row2-row1	1.09183	0.742
Var 36h NI row2-row1	0.97741	0.61
Var 60h I row2-row1	0.80632	0.285
Var 60h NI row2-row1	1.07259	0.904
Time course 0hI-0hNI	1.03594	0.833
Time course 12hI-12hNI	1.03586	0.738
Time course 36hI-36hNI	1.15256	0.063
Time course 60hI-60hNI	1.3232	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)	0.9194	0.33
transgenic ySAMdc/azygous control (breaker)	0.61988	0.142
transgenic ySAMdc/azygous control (red)	0.93227	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03052	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58784	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97017	1
Manapal/WT (break)	1.14946	0.381
Manapal/WT (red)	0.83764	0.199