Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.18.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82634	0.389
27DAP/17DAP	1.16848	0.849
39DAP/27DAP	1.58442	0.765
41DAP/39DAP	1.42688	0.183
42DAP/41DAP	1.1041	1
43DAP/42DAP	1.02781	0.937
47DAP/43DAP	0.84024	0.492
52DAP/47DAP	1.29154	0.562
57DAP/52DAP	1.15426	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85982	0.132
17DAP/reference	1.09727	0.546
27DAP/reference	0.91466	0.232
39DAP/reference	0.96698	0.651
41DAP/reference	0.98308	0.667
42DAP/reference	0.96772	0.169
43DAP/reference	0.93038	0.429
47DAP/reference	0.89828	0.055
52DAP/reference	0.95006	0.33
57DAP/reference	0.9573	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.27977	0.473
27DAP/17DAP	1.10032	0.969
39DAP/27DAP	1.09454	1
41DAP/39DAP	1.01661	1
42DAP/41DAP	1.05865	0.858
43DAP/42DAP	0.80689	0.027
47DAP/43DAP	1.24872	0.844
52DAP/47DAP	1.07112	0.816
57DAP/52DAP	1.62616	0.115
57DAP/7DAP	1.50919	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93044	0.402
17DAP/reference	1.45407	0.011
27DAP/reference	1.30192	0.131
39DAP/reference	1.0554	1
41DAP/reference	1.27789	0.27
42DAP/reference	1.00628	0.612
43DAP/reference	1.11119	0.432
47DAP/reference	1.07885	0.647
52DAP/reference	1.13399	0.286
57DAP/reference	1.39377	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82443	0.152
17DAP/reference	0.88353	0.279
27DAP/reference	0.87214	0.195
39DAP/reference	0.8963	0.097
41DAP/reference	0.84229	0.076
42DAP/reference	0.82833	0.108
43DAP/reference	0.8833	0.229
47DAP/reference	0.7398	0.011
52DAP/reference	0.96276	0.407
57DAP/reference	0.98364	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13815	0.366
17DAP/reference	1.02879	0.757
27DAP/reference	1.22238	0.115
39DAP/reference	1.06198	0.342
41DAP/reference	1.04406	0.984
42DAP/reference	1.01064	1
43DAP/reference	1.12272	0.679
47DAP/reference	0.83815	0.033
52DAP/reference	1.17038	0.749
57DAP/reference	0.78061	0.033

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99295	1
26DAP/20DAP	0.59943	0.512
34DAP/26DAP	1.29306	0.819
51DAP/34DAP	1.14231	0.73
52DAP/51DAP	1.20945	0.848
53DAP/52DAP	1.00195	0.983
55DAP/53DAP	0.73206	0.203
57DAP/55DAP	1.67169	0.364
62DAP/57DAP	1.07755	0.868
68DAP/62DAP	1.03787	0.945
68DAP/14DAP	0.90368	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04971	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.52444
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.14782
1-1-2/M82	0.99423	1
12-2/M82	0.94937	0.955
12-4/M82	0.91406	1
1-3/M82	0.84168	0.501
2-1-1/M82	1.37742
2-1/M82	N/A	N/A
2-6/M82	1.13477	0.452
3-2/M82	0.92362	1
4-1-1/M82	N/A	N/A
4-1/M82	1.00287	1
4-3-2/M82	0.87849	0.487
4-3/M82	N/A	N/A
5-3/M82	1.00219	1
6-2/M82	1.02093
6-3/M82	1.10392	1
7-1/M82	N/A	N/A
7-2/M82	0.99449	0.881
9-3-2/M82	1.10513

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	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	2.40853	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0528	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.21137	1
DC3000/delta hrp 24h	1.08856	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.01532	1
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	1.66135
Var 0h	0.80441	0.933
Var 12h I row2-row1	1.02063	0.736
Var 12h NI row2-row1	0.8682	1
Var 36h I row2-row1	1.01064	1
Var 36h NI row2-row1	1.06978	1
Var 60h I row2-row1	0.76364	0.285
Var 60h NI row2-row1	0.81524	0.977
Time course 0hI-0hNI	1.34094
Time course 12hI-12hNI	1.07723	1
Time course 36hI-36hNI	0.80879	0.005
Time course 60hI-60hNI	1.64865	0.187

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)	1.08971	0.931
transgenic ySAMdc/azygous control (breaker)	1.4614	1
transgenic ySAMdc/azygous control (red)	1.90524	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94603	0.256

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99768	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08353	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.76727	0.181