Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98398	0.801
27DAP/17DAP	1.0052	0.994
39DAP/27DAP	1.20991	0.52
41DAP/39DAP	0.72564	0.086
42DAP/41DAP	0.9767	1
43DAP/42DAP	0.94378	0.877
47DAP/43DAP	0.95241	0.716
52DAP/47DAP	1.29744	0.578
57DAP/52DAP	1.20454	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78374	0.034
17DAP/reference	0.70035	0.091
27DAP/reference	0.98691	0.779
39DAP/reference	0.72193	0.013
41DAP/reference	0.76322	0.008
42DAP/reference	0.88548	0.011
43DAP/reference	0.73148	0.247
47DAP/reference	0.86308	0.098
52DAP/reference	1.12547	0.695
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04429	0.923
27DAP/17DAP	0.95775	0.614
39DAP/27DAP	0.94141	0.482
41DAP/39DAP	1.07503	0.579
42DAP/41DAP	0.9267	0.387
43DAP/42DAP	1.01984	0.585
47DAP/43DAP	1.01493	0.963
52DAP/47DAP	0.95895	0.837
57DAP/52DAP	1.06865	0.79
57DAP/7DAP	0.98664	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41808	0.057
17DAP/reference	1.30208	0.009
27DAP/reference	1.14534	0.041
39DAP/reference	1.07123	0.222
41DAP/reference	1.13293	0.072
42DAP/reference	1.0706	0.405
43DAP/reference	1.04244	0.537
47DAP/reference	1.17504	0.093
52DAP/reference	1.24927	0.086
57DAP/reference	1.36833	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24526	0.695
17DAP/reference	0.75168	0.116
27DAP/reference	0.77022	0.084
39DAP/reference	0.94413	0.221
41DAP/reference	1.24572	0.199
42DAP/reference	0.91382	0.073
43DAP/reference	0.85295	0.125
47DAP/reference	1.07031	0.639
52DAP/reference	0.8265	0.156
57DAP/reference	0.82116	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.23862	0.037
17DAP/reference	1.13849	0.394
27DAP/reference	1.05074	0.531
39DAP/reference	1.15221	0.13
41DAP/reference	1.10187	0.077
42DAP/reference	3.05802	0.027
43DAP/reference	2.17447	0.044
47DAP/reference	0.84908	0.048
52DAP/reference	3.27367	0.079
57DAP/reference	1.19587	0.079

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99542	1
26DAP/20DAP	0.94879	N/A
34DAP/26DAP	0.98447	0.991
51DAP/34DAP	1.32356	0.038
52DAP/51DAP	1.13324	0.503
53DAP/52DAP	1.57978	0.048
55DAP/53DAP	0.81695	0.094
57DAP/55DAP	0.87455	0.496
62DAP/57DAP	0.42991	0.162
68DAP/62DAP	1.56885	0.036
68DAP/14DAP	2.06299	0.059

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.28818	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.33261	0.058
Mature Green Tomato/Ripe Tomato	1.06332	0.881
Immature Eggplant/Mature Eggplant	1.27694	0.23
Ripe Pepper/Ripe Tomato	0.46495	0.224
Mature Eggplant/Ripe Tomato	0.42606	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96658	0.944
1-1-2/M82	1.14296	1
12-2/M82	0.82059	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	1.04465	1
2-1/M82	N/A	N/A
2-6/M82	1.1504	0.405
3-2/M82	1.08247	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.42543	N/A
4-3-2/M82	1.28654	N/A
4-3/M82	N/A	N/A
5-3/M82	1.2835	0.572
6-2/M82	1.96756	N/A
6-3/M82	0.79139	N/A
7-1/M82	N/A	N/A
7-2/M82	1.40345	0.291
9-3-2/M82	1.08218	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98412	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.7868	N/A
IL1-4/WTpooled	1.05449	1
WT/WTpooled	0.97292	N/A

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	0.9623	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89084	1
DC3000/delta hrp 6h	1.11238	1
DC3000/delta hrp 12h	1.10653	1
DC3000/delta hrp 24h	0.87907	0.252

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95333	0.597
DC3000 delta B/DC3000 delta AB	1.14974	0.324

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03206	1
Exp 36h	1.02372	1
Exp 60h	1.01571	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99532	N/A
Var 0h	0.86695	0.933
Var 12h I row2-row1	0.98569	0.705
Var 12h NI row2-row1	1.10289	1
Var 36h I row2-row1	0.93097	1
Var 36h NI row2-row1	1.3507	1
Var 60h I row2-row1	3.81711	N/A
Var 60h NI row2-row1	1.29644	0.904
Time course 0hI-0hNI	0.97481	0.947
Time course 12hI-12hNI	0.92745	0.49
Time course 36hI-36hNI	0.9189	0.33
Time course 60hI-60hNI	0.69786	0.026

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)	0.91394	0.33
transgenic ySAMdc/azygous control (breaker)	0.72805	0.131
transgenic ySAMdc/azygous control (red)	1.23249	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17043	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96703	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94878	1
Manapal/WT (break)	0.84427	1
Manapal/WT (red)	0.8976	0.181