Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93256	0.496
27DAP/17DAP	0.98834	0.975
39DAP/27DAP	0.91215	0.549
41DAP/39DAP	1.17838	0.612
42DAP/41DAP	1.26631	0.912
43DAP/42DAP	0.93903	0.887
47DAP/43DAP	0.83067	0.439
52DAP/47DAP	1.62764	0.496
57DAP/52DAP	0.70684	0.527

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73613	0.046
17DAP/reference	0.60241	0.008
27DAP/reference	0.58623	0.011
39DAP/reference	0.61671	0.012
41DAP/reference	0.53911	0.008
42DAP/reference	0.64675	0.001
43DAP/reference	0.50975	0.012
47DAP/reference	0.51822	0.001
52DAP/reference	0.55837	0.013
57DAP/reference	0.576	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10238	0.326
27DAP/17DAP	0.94077	0.648
39DAP/27DAP	0.96994	0.784
41DAP/39DAP	1.11495	0.79
42DAP/41DAP	0.97284	0.737
43DAP/42DAP	1.04003	0.699
47DAP/43DAP	1.02994	0.973
52DAP/47DAP	1.15222	0.593
57DAP/52DAP	1.06509	0.745
57DAP/7DAP	0.91846	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92204	0.129
17DAP/reference	0.85483	0.024
27DAP/reference	0.83971	0.017
39DAP/reference	0.87036	0.015
41DAP/reference	0.87427	0.05
42DAP/reference	0.77584	0.023
43DAP/reference	0.77836	0.02
47DAP/reference	0.88851	0.383
52DAP/reference	0.71371	0.014
57DAP/reference	0.8264	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63728	0.009
17DAP/reference	0.71465	0.019
27DAP/reference	0.87885	0.269
39DAP/reference	0.75436	0.132
41DAP/reference	0.91581	0.34
42DAP/reference	0.83671	0.098
43DAP/reference	0.78118	0.095
47DAP/reference	0.79063	0.014
52DAP/reference	0.53703	0.006
57DAP/reference	0.5195	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91742	0.335
17DAP/reference	1.25853	0.365
27DAP/reference	0.84078	0.097
39DAP/reference	0.82605	0.031
41DAP/reference	0.89734	0.055
42DAP/reference	0.71375	0.036
43DAP/reference	0.81219	0.056
47DAP/reference	0.53416	0.004
52DAP/reference	0.52172	0.071
57DAP/reference	0.90611	0.221

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99182	1
26DAP/20DAP	0.87621	1
34DAP/26DAP	1.24974	0.542
51DAP/34DAP	0.94506	0.674
52DAP/51DAP	1.76307	0.071
53DAP/52DAP	0.96607	0.807
55DAP/53DAP	1.44335	0.162
57DAP/55DAP	0.74973	0.145
62DAP/57DAP	1.11685	0.515
68DAP/62DAP	0.99142	0.834
68DAP/14DAP	0.59368	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.60015	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.96894	0.058
Mature Green Tomato/Ripe Tomato	1.86651	0.577
Immature Eggplant/Mature Eggplant	0.31394	0.062
Ripe Pepper/Ripe Tomato	21.7315	1
Mature Eggplant/Ripe Tomato	8.73668	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99596	1
1-1-2/M82	0.86893	0.958
12-2/M82	1.10172	1
12-4/M82	1.00377	1
1-3/M82	1.08262	1
2-1-1/M82	1.02279	1
2-1/M82	0.82895	0.74
2-6/M82	1.06636	0.594
3-2/M82	0.95313	0.752
4-1-1/M82	1.03795	1
4-1/M82	0.94867	1
4-3-2/M82	1.00148	1
4-3/M82	1.18912	1
5-3/M82	1.03489	1
6-2/M82	0.98583	1
6-3/M82	0.98503	1
7-1/M82	0.92992	0.803
7-2/M82	1.06202	1
9-3-2/M82	0.75046	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.00914	1
IL2-6/WTpooled	1.05912	0.659
IL7-5/WTpooled	1.14232	1
IL7-3/WTpooled	0.79121	0.418
IL12-4/WTpooled	1.10354	0.839
IL1-4/WTpooled	0.96293	0.834
WT/WTpooled	1.07744	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	0.82691	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01324	0.921
DC3000/delta hrp 6h	1.15992	1
DC3000/delta hrp 12h	1.26028	1
DC3000/delta hrp 24h	1.03069	0.71

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04219	0.556
DC3000 delta B/DC3000 delta AB	0.96655	0.766

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0267	1
Exp 36h	0.88681	0.749
Exp 60h	0.79219	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99467	1
Var 0h	0.43281	1
Var 12h I row2-row1	0.96261	0.948
Var 12h NI row2-row1	0.93589	0.546
Var 36h I row2-row1	0.97747	1
Var 36h NI row2-row1	1.2356	0.482
Var 60h I row2-row1	1.06707	1
Var 60h NI row2-row1	1.15651	0.904
Time course 0hI-0hNI	0.89634	0.516
Time course 12hI-12hNI	1.00034	1
Time course 36hI-36hNI	0.74759	0.043
Time course 60hI-60hNI	0.40199	0.007

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)	0.91259	0.567
transgenic ySAMdc/azygous control (breaker)	2.01493	0.178
transgenic ySAMdc/azygous control (red)	1.36299	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.64689	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.92703	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	25.4733	0.083
Manapal/WT (break)	4.53359	0.13
Manapal/WT (red)	2.00034	0.222