Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.4.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.5503	0.015
27DAP/17DAP	0.5918	0.086
39DAP/27DAP	0.84934	0.544
41DAP/39DAP	0.80442	0.385
42DAP/41DAP	1.08665	0.931
43DAP/42DAP	1.42464	0.16
47DAP/43DAP	0.68273	0.141
52DAP/47DAP	0.79578	0.466
57DAP/52DAP	1.03106	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47773	0.008
17DAP/reference	1.1311	0.061
27DAP/reference	1.3334	0.01
39DAP/reference	0.97308	0.734
41DAP/reference	0.77447	0.021
42DAP/reference	1.16738	0.065
43DAP/reference	0.98284	0.728
47DAP/reference	0.90917	0.083
52DAP/reference	0.96121	0.438
57DAP/reference	1.07672	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72787	0.042
27DAP/17DAP	1.26795	0.231
39DAP/27DAP	0.59644	0.032
41DAP/39DAP	0.32865	0.013
42DAP/41DAP	1.17804	0.727
43DAP/42DAP	1.92895	0.014
47DAP/43DAP	0.74973	0.018
52DAP/47DAP	0.67706	0.042
57DAP/52DAP	0.93863	0.673
57DAP/7DAP	0.17969	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.0569	0.024
17DAP/reference	1.48144	0.008
27DAP/reference	1.16671	0.16
39DAP/reference	1.079	0.166
41DAP/reference	1.19271	0.147
42DAP/reference	1.05584	0.405
43DAP/reference	1.21797	0.408
47DAP/reference	0.97679	0.671
52DAP/reference	1.00282	0.802
57DAP/reference	0.92831	0.191

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20857	0.732
17DAP/reference	0.97442	0.642
27DAP/reference	1.08229	0.562
39DAP/reference	0.85803	0.136
41DAP/reference	1.11238	0.688
42DAP/reference	1.15343	0.091
43DAP/reference	0.57348	0.007
47DAP/reference	1.05897	0.712
52DAP/reference	0.91021	0.259
57DAP/reference	0.73535	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.23526	0.016
17DAP/reference	1.59066	0.279
27DAP/reference	2.15916	0.014
39DAP/reference	1.32012	0.017
41DAP/reference	1.17189	0.089
42DAP/reference	1.2527	0.209
43DAP/reference	1.24888	0.081
47DAP/reference	1.03399	1
52DAP/reference	1.05131	0.724
57DAP/reference	1.48956	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11248	0.966
26DAP/20DAP	1.58929	0.102
34DAP/26DAP	0.95324	0.898
51DAP/34DAP	1.31272	0.054
52DAP/51DAP	0.86701	1
53DAP/52DAP	0.78552	0.055
55DAP/53DAP	0.39893	0.016
57DAP/55DAP	0.56373	0.03
62DAP/57DAP	26.3594
68DAP/62DAP	2.28509	0.247
68DAP/14DAP	1.76054	0.036

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.1142	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.53846	0.058
Mature Green Tomato/Ripe Tomato	8.78895	0.015
Immature Eggplant/Mature Eggplant	0.22964	0.057
Ripe Pepper/Ripe Tomato	26.6883	0.256
Mature Eggplant/Ripe Tomato	22.1094	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.1537	1
12-2/M82	0.83264	0.955
12-4/M82	1.01299	1
1-3/M82	1.76551
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	3.59293
3-2/M82	0.56234
4-1-1/M82	N/A	N/A
4-1/M82	0.50351
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.75053	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.47694	0.803
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03796	0.493
IL2-6/WTpooled	1.18004	0.659
IL7-5/WTpooled	0.8987	1
IL7-3/WTpooled	0.81507	0.418
IL12-4/WTpooled	1.17924	1
IL1-4/WTpooled	0.908	0.699
WT/WTpooled	1.07171	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	0.85776	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91643	1
DC3000/delta hrp 6h	0.8089	0.95
DC3000/delta hrp 12h	1.13535	1
DC3000/delta hrp 24h	0.38335	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42596	0.024
DC3000 delta B/DC3000 delta AB	0.45561	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08521	1
Exp 36h	0.74337	0.471
Exp 60h	0.58836	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.99816	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.97312	0.614
transgenic ySAMdc/azygous control (breaker)	1.10378	1
transgenic ySAMdc/azygous control (red)	3.33478	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.79266	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.37805	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.29643	0.307
Manapal/WT (break)	2.58655	0.183
Manapal/WT (red)	2.08342	0.15