Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.14.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98865	0.83
27DAP/17DAP	0.75657	0.353
39DAP/27DAP	0.93551	0.641
41DAP/39DAP	0.62495	0.062
42DAP/41DAP	1.00811	1
43DAP/42DAP	1.06749	1
47DAP/43DAP	0.62499	0.079
52DAP/47DAP	0.531	0.049
57DAP/52DAP	0.82717	0.687

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70616	0.013
17DAP/reference	1.48704	0.045
27DAP/reference	1.54983	0.032
39DAP/reference	1.68984	0.077
41DAP/reference	1.25644	0.073
42DAP/reference	1.25642	0.001
43DAP/reference	0.91739	0.071
47DAP/reference	0.8446	0.046
52DAP/reference	0.61715	0.014
57DAP/reference	0.6991	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16104	0.176
27DAP/17DAP	0.87059	0.172
39DAP/27DAP	0.75214	0.097
41DAP/39DAP	0.96472	0.923
42DAP/41DAP	0.90746	0.214
43DAP/42DAP	0.7826	0.022
47DAP/43DAP	0.81167	0.014
52DAP/47DAP	0.86707	0.378
57DAP/52DAP	0.82873	0.241
57DAP/7DAP	0.56343	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.61068	0.025
17DAP/reference	1.48263	0.014
27DAP/reference	1.10535	0.371
39DAP/reference	1.0538	0.779
41DAP/reference	0.87533	0.079
42DAP/reference	0.90425	0.136
43DAP/reference	1.00865	0.764
47DAP/reference	0.9653	0.671
52DAP/reference	1.10073	0.526
57DAP/reference	1.3795	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20719	0.449
17DAP/reference	1.6074	0.012
27DAP/reference	1.19731	0.136
39DAP/reference	0.88515	0.152
41DAP/reference	0.873	0.152
42DAP/reference	0.99196	0.655
43DAP/reference	0.84911	0.14
47DAP/reference	0.85513	0.066
52DAP/reference	0.74523	0.005
57DAP/reference	0.58255	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.14182	0.015
17DAP/reference	1.98566	0.169
27DAP/reference	1.62395	0.02
39DAP/reference	1.80299	0.007
41DAP/reference	1.55743	0.009
42DAP/reference	1.39851	0.046
43DAP/reference	1.40943	0.019
47DAP/reference	1.15711	0.093
52DAP/reference	1.08233	0.888
57DAP/reference	1.33238	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18086	0.966
26DAP/20DAP	0.70087	0.512
34DAP/26DAP	1.00942	1
51DAP/34DAP	1.30526	0.898
52DAP/51DAP	0.92627	1
53DAP/52DAP	0.95942	0.83
55DAP/53DAP	1.12686	0.671
57DAP/55DAP	1.09738	0.906
62DAP/57DAP	0.9507	0.871
68DAP/62DAP	0.58228	0.055
68DAP/14DAP	1.1095	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.42373	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.8155	0.058
Mature Green Tomato/Ripe Tomato	7.89595	0.015
Immature Eggplant/Mature Eggplant	0.50079	0.062
Ripe Pepper/Ripe Tomato	1.37992	1
Mature Eggplant/Ripe Tomato	6.21864	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25829	0.455
1-1-2/M82	1.01983	1
12-2/M82	0.70105	0.727
12-4/M82	1.26022	1
1-3/M82	1.01261	1
2-1-1/M82	0.91931	1
2-1/M82	0.35919
2-6/M82	2.3214	0.345
3-2/M82	N/A	N/A
4-1-1/M82	1.2058	1
4-1/M82	0.85936	0.867
4-3-2/M82	2.05669	0.241
4-3/M82	1.30303	1
5-3/M82	0.88446	0.447
6-2/M82	1.22625
6-3/M82	0.93644	1
7-1/M82	1.21623
7-2/M82	N/A	N/A
9-3-2/M82	1.86437	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93732	1
IL2-6/WTpooled	1.07459	0.46
IL7-5/WTpooled	1.12585	1
IL7-3/WTpooled	0.91562	1
IL12-4/WTpooled	1.07369	0.839
IL1-4/WTpooled	0.96018	0.699
WT/WTpooled	0.92644	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	0.83229	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00132	1
DC3000/delta hrp 6h	1.02399	1
DC3000/delta hrp 12h	1.26249	1
DC3000/delta hrp 24h	0.6591	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79191	0.036
DC3000 delta B/DC3000 delta AB	0.76051	0.028

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00573	1
Exp 36h	0.6893	0.539
Exp 60h	0.55271	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99719	1
Var 0h	1.03671	0.936
Var 12h I row2-row1	0.6986	0.338
Var 12h NI row2-row1	0.84426	0.546
Var 36h I row2-row1	0.76872	0.805
Var 36h NI row2-row1	1.17001	1
Var 60h I row2-row1	1.12793	0.543
Var 60h NI row2-row1	0.94964	1
Time course 0hI-0hNI	1.01935	0.852
Time course 12hI-12hNI	1.01414	0.836
Time course 36hI-36hNI	0.85879	0.033
Time course 60hI-60hNI	0.15575	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)	1.00828	0.863
transgenic ySAMdc/azygous control (breaker)	1.08689	1
transgenic ySAMdc/azygous control (red)	1.0902	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89654	0.047

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33469	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.36511	0.09
Manapal/WT (break)	3.23002	0.13
Manapal/WT (red)	1.84523	0.15