Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99983	0.876
27DAP/17DAP	0.86377	0.665
39DAP/27DAP	0.88774	0.522
41DAP/39DAP	1.11214	0.545
42DAP/41DAP	1.12585	1
43DAP/42DAP	0.9242	0.864
47DAP/43DAP	0.79477	0.41
52DAP/47DAP	1.43937	0.538
57DAP/52DAP	0.7716	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1683	0.421
17DAP/reference	1.31651	0.369
27DAP/reference	0.44348
39DAP/reference	1.60656	0.722
41DAP/reference	1.40266	0.241
42DAP/reference	1.67761	0.467
43DAP/reference	0.47279
47DAP/reference	1.62499	0.001
52DAP/reference	1.26409	0.84
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07553	0.923
27DAP/17DAP	0.89445	0.418
39DAP/27DAP	0.88585	0.316
41DAP/39DAP	0.94997	0.861
42DAP/41DAP	0.95156	0.603
43DAP/42DAP	0.87211	0.041
47DAP/43DAP	0.94415	0.687
52DAP/47DAP	0.98682	0.925
57DAP/52DAP	1.15078	0.486
57DAP/7DAP	1.03012	0.153

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77902	0.059
17DAP/reference	0.77669	0.011
27DAP/reference	0.81588	0.011
39DAP/reference	0.703	0.011
41DAP/reference	0.67215	0.022
42DAP/reference	0.64759	0.01
43DAP/reference	0.70961	0.016
47DAP/reference	0.7639	0.168
52DAP/reference	0.66489	0.022
57DAP/reference	0.6971	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35183	0.582
17DAP/reference	1.26278	0.961
27DAP/reference	1.16951	0.745
39DAP/reference	1.81809
41DAP/reference	2.03206	0.005
42DAP/reference	0.46152
43DAP/reference	1.23037	0.532
47DAP/reference	1.10732	0.916
52DAP/reference	2.16438	0.069
57DAP/reference	1.11031	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75344	0.039
17DAP/reference	0.90246	0.488
27DAP/reference	0.7476	0.025
39DAP/reference	0.72824	0.012
41DAP/reference	0.76472	0.022
42DAP/reference	0.80179	0.087
43DAP/reference	0.77516	0.016
47DAP/reference	2.59961	0.007
52DAP/reference	1.3025	0.664
57DAP/reference	0.57785	0.118

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.75956	1
26DAP/20DAP	1.01717	1
34DAP/26DAP	1.03993	1
51DAP/34DAP	0.90659	0.598
52DAP/51DAP	0.86823	1
53DAP/52DAP	1.01741	0.921
55DAP/53DAP	0.76435	0.325
57DAP/55DAP	1.11508	0.805
62DAP/57DAP	1.51063	0.767
68DAP/62DAP	0.8268	0.29
68DAP/14DAP	1.46184	0.025

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.53698	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.63927	0.095
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.21347
Mature Eggplant/Ripe Tomato	1.53197

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85676	0.536
1-1-2/M82	0.83329	0.761
12-2/M82	1.03239	1
12-4/M82	0.88862	1
1-3/M82	0.80249	0.378
2-1-1/M82	0.94048	1
2-1/M82	N/A	N/A
2-6/M82	1.43958	0.329
3-2/M82	0.87472
4-1-1/M82	N/A	N/A
4-1/M82	1.30836
4-3-2/M82	N/A	N/A
4-3/M82	1.04673
5-3/M82	0.95866	0.364
6-2/M82	0.8382	1
6-3/M82	1.03306	1
7-1/M82	N/A	N/A
7-2/M82	1.03516	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9259	1
IL2-6/WTpooled	1.03851	1
IL7-5/WTpooled	0.83739	1
IL7-3/WTpooled	0.90678	1
IL12-4/WTpooled	0.70727	0.71
IL1-4/WTpooled	0.97741	0.562
WT/WTpooled	1.15661	0.999

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	0.9812	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88523	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.95292	1
DC3000/delta hrp 24h	0.81973	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65448	0.024
DC3000 delta B/DC3000 delta AB	0.62824	0.021

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	0.72953	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97515	1
Var 0h	0.93003	1
Var 12h I row2-row1	0.78648	0.418
Var 12h NI row2-row1	1.02993	1
Var 36h I row2-row1	1.18243	1
Var 36h NI row2-row1	1.55263	1
Var 60h I row2-row1	1.12168	0.543
Var 60h NI row2-row1	1.11606	0.904
Time course 0hI-0hNI	0.98153	0.945
Time course 12hI-12hNI	1.04713	0.785
Time course 36hI-36hNI	0.8522	0.183
Time course 60hI-60hNI	0.20651	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.86339	0.183
Manapal/WT (red)	1.34163	0.413