Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.15.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27699	0.498
27DAP/17DAP	0.79123	0.41
39DAP/27DAP	1.44076	0.149
41DAP/39DAP	0.65782	0.053
42DAP/41DAP	0.74861	0.774
43DAP/42DAP	0.92897	0.887
47DAP/43DAP	0.41593	0.049
52DAP/47DAP	0.88257	0.729
57DAP/52DAP	0.94262	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0098	0.743
17DAP/reference	0.90278	0.158
27DAP/reference	1.27004	0.175
39DAP/reference	0.81425	0.035
41DAP/reference	0.63757	0.008
42DAP/reference	0.83357	0.02
43DAP/reference	0.84373	0.2
47DAP/reference	0.95078	0.322
52DAP/reference	1.20402	0.878
57DAP/reference	1.57216	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.86662	0.036
27DAP/17DAP	0.7269	0.179
39DAP/27DAP	0.88943	0.35
41DAP/39DAP	1.49423	0.705
42DAP/41DAP	0.99637	0.816
43DAP/42DAP	0.52885	0.022
47DAP/43DAP	0.89786	0.235
52DAP/47DAP	0.85726	0.3
57DAP/52DAP	0.61994	0.106
57DAP/7DAP	0.42837	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.79693	0.024
17DAP/reference	2.13539	0.006
27DAP/reference	1.76197	0.01
39DAP/reference	2.40966	0.005
41DAP/reference	2.08792	0.008
42DAP/reference	1.46633	0.03
43DAP/reference	1.15573	0.289
47DAP/reference	1.36396	0.057
52DAP/reference	1.1157	0.183
57DAP/reference	1.14462	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06173	0.852
17DAP/reference	1.01913	0.92
27DAP/reference	1.1373	0.265
39DAP/reference	1.16283	0.15
41DAP/reference	1.37959	0.012
42DAP/reference	1.08305	0.17
43DAP/reference	0.80572	0.111
47DAP/reference	0.96803	0.434
52DAP/reference	0.86744	0.04
57DAP/reference	0.56755	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81043	0.021
17DAP/reference	1.24059	0.578
27DAP/reference	1.42181	0.035
39DAP/reference	1.56373	0.007
41DAP/reference	1.36068	0.012
42DAP/reference	0.86783	0.22
43DAP/reference	0.94656	0.416
47DAP/reference	0.73922	0.028
52DAP/reference	0.62445	0.057
57DAP/reference	2.01707	0.121

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99829	1
26DAP/20DAP	0.51461
34DAP/26DAP	0.76226	0.472
51DAP/34DAP	0.99408	0.893
52DAP/51DAP	1.09494	1
53DAP/52DAP	0.8012	0.358
55DAP/53DAP	1.11129	0.534
57DAP/55DAP	0.79169	0.37
62DAP/57DAP	0.96984	0.994
68DAP/62DAP	1.95357	0.132
68DAP/14DAP	2.09488	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	8.71511	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.06889	0.015
Immature Eggplant/Mature Eggplant	0.41597	0.062
Ripe Pepper/Ripe Tomato	0.08143	0.224
Mature Eggplant/Ripe Tomato	1.18006	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01943	1
1-1-2/M82	1.21154	1
12-2/M82	0.91365	0.955
12-4/M82	0.85431
1-3/M82	N/A	N/A
2-1-1/M82	0.87382
2-1/M82	0.87348	0.519
2-6/M82	1.3018	0.395
3-2/M82	1.21793	0.84
4-1-1/M82	1.65109	1
4-1/M82	2.55479	1
4-3-2/M82	1.45748
4-3/M82	0.53282
5-3/M82	0.99682	1
6-2/M82	1.87609
6-3/M82	0.98982	1
7-1/M82	1.70282	0.539
7-2/M82	2.4719	0.324
9-3-2/M82	1.72873

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99356	1
IL2-6/WTpooled	1.07648	0.788
IL7-5/WTpooled	0.77499
IL7-3/WTpooled	0.99679	1
IL12-4/WTpooled	0.97408	0.71
IL1-4/WTpooled	1.63818
WT/WTpooled	1.02366	1

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	0.93096	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99163	1
DC3000/delta hrp 6h	0.93253	0.95
DC3000/delta hrp 12h	0.89282	1
DC3000/delta hrp 24h	1.35444	0.05

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24911	0.05
DC3000 delta B/DC3000 delta AB	1.21482	0.162

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03327	1
Exp 36h	0.8214	0.661
Exp 60h	0.92405	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03089	1
Var 0h	0.87576	0.933
Var 12h I row2-row1	0.84143	0.31
Var 12h NI row2-row1	1.09621	0.649
Var 36h I row2-row1	1.11202	0.41
Var 36h NI row2-row1	0.95302	0.706
Var 60h I row2-row1	0.78941	0.374
Var 60h NI row2-row1	0.82654	0.304
Time course 0hI-0hNI	1.06855	0.799
Time course 12hI-12hNI	1.02016	0.836
Time course 36hI-36hNI	1.17737	0.128
Time course 60hI-60hNI	1.61298	0.008

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)	0.67632	0.246
transgenic ySAMdc/azygous control (breaker)	0.14975	0.119
transgenic ySAMdc/azygous control (red)	2.38237	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01766	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79175	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.64189	0.105
Manapal/WT (break)	0.9847	1
Manapal/WT (red)	1.58376	0.222