Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19413	0.77
27DAP/17DAP	1.24259	0.881
39DAP/27DAP	1.102	0.768
41DAP/39DAP	0.61367	0.094
42DAP/41DAP	0.7986	0.774
43DAP/42DAP	1.02157	0.909
47DAP/43DAP	0.76768	0.345
52DAP/47DAP	0.75761	0.609
57DAP/52DAP	1.44217	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96831	0.503
17DAP/reference	0.99117	0.819
27DAP/reference	0.87928	0.134
39DAP/reference	0.85643	0.155
41DAP/reference	0.8085	0.065
42DAP/reference	0.80066	0.002
43DAP/reference	0.9575	0.5
47DAP/reference	0.72657	0.001
52DAP/reference	0.64785	0.012
57DAP/reference	0.75393	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.48959	0.02
27DAP/17DAP	1.18748	0.74
39DAP/27DAP	0.66584	0.056
41DAP/39DAP	0.60823	0.047
42DAP/41DAP	1.17252	0.947
43DAP/42DAP	1.31971	0.162
47DAP/43DAP	0.84295	0.067
52DAP/47DAP	0.92836	0.719
57DAP/52DAP	0.99071	0.841
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33156	0.032
17DAP/reference	1.06069	0.147
27DAP/reference	0.9494	0.117
39DAP/reference	0.92457	0.126
41DAP/reference	0.70497	0.012
42DAP/reference	0.74961	0.01
43DAP/reference	0.77716	0.011
47DAP/reference	0.75394	0.044
52DAP/reference	0.85155	0.019
57DAP/reference	0.97046	0.367

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93297	0.426
17DAP/reference	0.84567	0.086
27DAP/reference	0.96275	0.483
39DAP/reference	0.95147	0.306
41DAP/reference	0.98262	0.505
42DAP/reference	0.96214	0.392
43DAP/reference	0.59437	0.005
47DAP/reference	0.80231	0.021
52DAP/reference	0.62614	0.006
57DAP/reference	0.46274	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.84613	0.016
17DAP/reference	1.83352	0.013
27DAP/reference	1.43876	0.02
39DAP/reference	1.25954	0.029
41DAP/reference	1.10649	0.162
42DAP/reference	0.93503	0.445
43DAP/reference	0.96608	0.568
47DAP/reference	0.74743	0.005
52DAP/reference	0.80365	0.208
57DAP/reference	0.91305	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03553	0.966
26DAP/20DAP	1.01024	1
34DAP/26DAP	1.19897	1
51DAP/34DAP	0.68684	0.117
52DAP/51DAP	0.98149	1
53DAP/52DAP	0.69452	0.393
55DAP/53DAP	0.28831	0.036
57DAP/55DAP	1.00379	0.88
62DAP/57DAP	1.273	0.024
68DAP/62DAP	0.96741	0.81
68DAP/14DAP	0.97796	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.61805	0.059

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.55412	0.113
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	0.41585	0.062
Ripe Pepper/Ripe Tomato	1.76669	0.256
Mature Eggplant/Ripe Tomato	2.64924	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03786	0.526
1-1-2/M82	0.90084	1
12-2/M82	0.87439	0.955
12-4/M82	0.97645
1-3/M82	0.82679
2-1-1/M82	0.89918	1
2-1/M82	0.82055
2-6/M82	0.99654	1
3-2/M82	1.16148
4-1-1/M82	1.05968
4-1/M82	0.97689
4-3-2/M82	1.10053
4-3/M82	1.17509
5-3/M82	1.12128	1
6-2/M82	1.0414
6-3/M82	1.08186	1
7-1/M82	N/A	N/A
7-2/M82	1.0956	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11171	0.277
IL2-6/WTpooled	1.12986	0.419
IL7-5/WTpooled	1.06403	0.792
IL7-3/WTpooled	1.02944	1
IL12-4/WTpooled	0.93115	0.71
IL1-4/WTpooled	1.06625	1
WT/WTpooled	1.0699	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	0.84418	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02849	0.921
DC3000/delta hrp 6h	1.0702	1
DC3000/delta hrp 12h	1.01708
DC3000/delta hrp 24h	0.91225	0.274

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54117	0.024
DC3000 delta B/DC3000 delta AB	0.53977	0.024

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	1.00322	1
Var 0h	0.88734	0.933
Var 12h I row2-row1	0.94993	0.705
Var 12h NI row2-row1	0.8323	0.488
Var 36h I row2-row1	0.98341	1
Var 36h NI row2-row1	1.18054	1
Var 60h I row2-row1	0.89134	0.832
Var 60h NI row2-row1	1.06845	0.904
Time course 0hI-0hNI	1.09614	0.63
Time course 12hI-12hNI	0.94558	0.497
Time course 36hI-36hNI	0.83047	0.051
Time course 60hI-60hNI	0.34221	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)	1.12465	0.699
transgenic ySAMdc/azygous control (breaker)	3.02661	0.166
transgenic ySAMdc/azygous control (red)	1.1885	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87253	0.181

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13527	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.62963	0.096
Manapal/WT (break)	3.85302	0.13
Manapal/WT (red)	3.99966	0.133