Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13838	0.697
27DAP/17DAP	0.73168	0.217
39DAP/27DAP	0.86711	0.549
41DAP/39DAP	0.76294	0.215
42DAP/41DAP	0.85983	0.774
43DAP/42DAP	1.17652	0.712
47DAP/43DAP	1.20254	0.595
52DAP/47DAP	0.82475	0.518
57DAP/52DAP	1.03917	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85837	0.149
17DAP/reference	0.69339	0.012
27DAP/reference	0.83706	0.152
39DAP/reference	0.75211	0.085
41DAP/reference	0.5592	0.01
42DAP/reference	0.80164	0.011
43DAP/reference	0.77965	0.073
47DAP/reference	0.83167	0.055
52DAP/reference	1.04526	0.709
57DAP/reference	1.22462	0.02

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18492	0.482
27DAP/17DAP	0.86177	0.724
39DAP/27DAP	0.49059	0.028
41DAP/39DAP	1.26327	0.439
42DAP/41DAP	1.09222	0.601
43DAP/42DAP	0.79865	0.031
47DAP/43DAP	0.99076	0.954
52DAP/47DAP	0.94755	0.837
57DAP/52DAP	0.89947	0.507
57DAP/7DAP	0.48887	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47774	0.041
17DAP/reference	1.01009	1
27DAP/reference	0.8192	0.017
39DAP/reference	0.64692	0.023
41DAP/reference	0.49586	0.011
42DAP/reference	0.44171	0.01
43DAP/reference	0.43964	0.01
47DAP/reference	0.62981	0.057
52DAP/reference	0.68282	0.027
57DAP/reference	0.58469	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80727	0.032
17DAP/reference	0.78451	0.035
27DAP/reference	0.91599	0.34
39DAP/reference	0.96656	0.442
41DAP/reference	0.99896	0.649
42DAP/reference	0.85683	0.055
43DAP/reference	0.39472	0.002
47DAP/reference	0.64808	0.009
52DAP/reference	0.75742	0.007
57DAP/reference	0.50176	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.51634	0.015
17DAP/reference	1.92603	0.115
27DAP/reference	1.61048	0.02
39DAP/reference	1.19766	0.069
41DAP/reference	1.116	0.108
42DAP/reference	0.90691	0.361
43DAP/reference	1.04414	0.949
47DAP/reference	0.78165	0.045
52DAP/reference	0.57656	0.049
57DAP/reference	1.75464	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8632	0.807
26DAP/20DAP	0.91611	1
34DAP/26DAP	1.07195	1
51DAP/34DAP	0.81976	0.109
52DAP/51DAP	1.18442	0.606
53DAP/52DAP	1.13179
55DAP/53DAP	1.09208	0.982
57DAP/55DAP	0.8534	0.464
62DAP/57DAP	1.41887	0.868
68DAP/62DAP	1.17594	0.5
68DAP/14DAP	1.79837	0.042

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41399	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.30971	0.058
Mature Green Tomato/Ripe Tomato	2.72791	0.016
Immature Eggplant/Mature Eggplant	0.50257	0.063
Ripe Pepper/Ripe Tomato	5.29704	1
Mature Eggplant/Ripe Tomato	9.58888	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0919
12-2/M82	N/A	N/A
12-4/M82	1.02011
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.97277	0.487
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.90826	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88496	0.243
IL2-6/WTpooled	1.04213	1
IL7-5/WTpooled	0.86498	1
IL7-3/WTpooled	0.88639	1
IL12-4/WTpooled	1.0099	1
IL1-4/WTpooled	0.91146	0.699
WT/WTpooled	1.12369	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	1.04613	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93491	1
DC3000/delta hrp 6h	1.07456	1
DC3000/delta hrp 12h	1.31109	1
DC3000/delta hrp 24h	0.61122	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.47258	0.023
DC3000 delta B/DC3000 delta AB	0.47617	0.02

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	0.94482	1
Var 0h	0.5681	0.782
Var 12h I row2-row1	0.72258	0.338
Var 12h NI row2-row1	0.85208	0.627
Var 36h I row2-row1	0.84012	0.805
Var 36h NI row2-row1	1.29613	1
Var 60h I row2-row1	1.23382	0.562
Var 60h NI row2-row1	1.06309	1
Time course 0hI-0hNI	0.96587	0.839
Time course 12hI-12hNI	0.97459	0.855
Time course 36hI-36hNI	0.81409	0.037
Time course 60hI-60hNI	0.16048	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)	1.19494	0.654
transgenic ySAMdc/azygous control (breaker)	4.094	0.165
transgenic ySAMdc/azygous control (red)	1.10636	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.63386	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.67584	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	9.04868	0.083
Manapal/WT (break)	11.5269	0.13
Manapal/WT (red)	4.41061	0.142