Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.859	0.347
27DAP/17DAP	0.97953	1
39DAP/27DAP	1.07102	0.946
41DAP/39DAP	0.90985	0.619
42DAP/41DAP	1.06458	1
43DAP/42DAP	1.03191	1
47DAP/43DAP	0.77895	0.314
52DAP/47DAP	1.31451	0.515
57DAP/52DAP	0.98451	0.974

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94418	0.277
17DAP/reference	0.72723	0.007
27DAP/reference	0.95887	0.514
39DAP/reference	0.81441	0.026
41DAP/reference	0.64913	0.008
42DAP/reference	0.88595	0.052
43DAP/reference	0.84627	0.118
47DAP/reference	0.9485	0.322
52DAP/reference	1.22635	0.335
57DAP/reference	1.35117	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04994	0.899
27DAP/17DAP	0.95718	0.854
39DAP/27DAP	0.82905	0.207
41DAP/39DAP	0.98867	0.997
42DAP/41DAP	1.2191	0.46
43DAP/42DAP	1.08218	0.554
47DAP/43DAP	1.08796	0.464
52DAP/47DAP	0.98762	0.93
57DAP/52DAP	1.11182	0.65
57DAP/7DAP	0.77007	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26798	0.08
17DAP/reference	1.14718	0.18
27DAP/reference	1.11271	0.197
39DAP/reference	0.87001	0.034
41DAP/reference	1.07	0.389
42DAP/reference	1.01813	1
43DAP/reference	0.81306	0.018
47DAP/reference	1.02891	0.901
52DAP/reference	1.05801	0.781
57DAP/reference	1.18528	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74174	0.014
17DAP/reference	0.82028	0.022
27DAP/reference	0.96646	0.467
39DAP/reference	1.00185	0.603
41DAP/reference	1.02687	0.981
42DAP/reference	0.93493	0.321
43DAP/reference	0.73343	0.021
47DAP/reference	0.79122	0.013
52DAP/reference	0.83904	0.005
57DAP/reference	0.66296	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02416	0.939
17DAP/reference	0.95816	0.508
27DAP/reference	0.9959	0.763
39DAP/reference	0.97606	0.544
41DAP/reference	1.01105	1
42DAP/reference	0.88763	0.071
43DAP/reference	1.06991	0.84
47DAP/reference	0.88266	0.125
52DAP/reference	0.93698	0.529
57DAP/reference	1.42867	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00594	1
26DAP/20DAP	1.31061	0.813
34DAP/26DAP	1.54218	0.542
51DAP/34DAP	0.70946	0.095
52DAP/51DAP	0.96906	1
53DAP/52DAP	0.76789	0.186
55DAP/53DAP	1.35557	0.576
57DAP/55DAP	0.85444	0.499
62DAP/57DAP	1.54175	0.622
68DAP/62DAP	1.86046	0.06
68DAP/14DAP	2.04927	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.55511	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.39984	0.058
Mature Green Tomato/Ripe Tomato	1.09162	0.038
Immature Eggplant/Mature Eggplant	1.07601	0.633
Ripe Pepper/Ripe Tomato	0.36467	0.224
Mature Eggplant/Ripe Tomato	0.81769	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12258
1-1-2/M82	1.08497	0.972
12-2/M82	0.98339	1
12-4/M82	N/A	N/A
1-3/M82	1.13444
2-1-1/M82	1.11036	1
2-1/M82	N/A	N/A
2-6/M82	0.74968	1
3-2/M82	0.72025
4-1-1/M82	0.49037
4-1/M82	0.81063
4-3-2/M82	1.04478	1
4-3/M82	N/A	N/A
5-3/M82	1.38941	1
6-2/M82	1.09117
6-3/M82	0.67152
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.9839	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08175	0.419
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88227	0.418
IL12-4/WTpooled	1.10824	0.531
IL1-4/WTpooled	0.69398	0.562
WT/WTpooled	1.02074	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	1.04611	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97763	1
DC3000/delta hrp 6h	0.94774	0.95
DC3000/delta hrp 12h	0.97864	1
DC3000/delta hrp 24h	1.18268	0.308

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06389
DC3000 delta B/DC3000 delta AB	1.04704	0.738

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	1.05542	1
Var 0h	1.17296	0.594
Var 12h I row2-row1	0.90892	0.338
Var 12h NI row2-row1	1.11254	1
Var 36h I row2-row1	1.11715	1
Var 36h NI row2-row1	1.0175	1
Var 60h I row2-row1	0.92128	0.832
Var 60h NI row2-row1	1.02577	1
Time course 0hI-0hNI	0.92026	0.247
Time course 12hI-12hNI	0.97619	0.841
Time course 36hI-36hNI	0.86325	0.101
Time course 60hI-60hNI	0.56911	0.006

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)	0.9741	0.662
transgenic ySAMdc/azygous control (breaker)	0.91699	0.173
transgenic ySAMdc/azygous control (red)	0.91572	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97452	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.02287	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80079	0.172
Manapal/WT (break)	1.03151	1
Manapal/WT (red)	1.32187	0.222