Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28762	0.291
27DAP/17DAP	0.61806	0.087
39DAP/27DAP	1.08993	1
41DAP/39DAP	0.57031	0.041
42DAP/41DAP	1.15688	0.852
43DAP/42DAP	1.07265	1
47DAP/43DAP	0.95975	0.84
52DAP/47DAP	0.6188	0.067
57DAP/52DAP	1.01366	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91221	0.118
17DAP/reference	1.04474	0.27
27DAP/reference	1.02295	0.721
39DAP/reference	0.99097	0.855
41DAP/reference	1.00214	1
42DAP/reference	0.91958	0.085
43DAP/reference	0.9679	0.631
47DAP/reference	0.89341	0.005
52DAP/reference	0.78345	0.023
57DAP/reference	0.91175	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46825	0.041
27DAP/17DAP	0.80317	0.144
39DAP/27DAP	1.02708	1
41DAP/39DAP	0.79822	0.246
42DAP/41DAP	1.27878	0.273
43DAP/42DAP	1.13011	0.147
47DAP/43DAP	0.87528	0.319
52DAP/47DAP	1.0503	0.823
57DAP/52DAP	0.74467	0.187
57DAP/7DAP	0.89492	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09314	0.427
17DAP/reference	0.90168	0.082
27DAP/reference	0.9511	0.402
39DAP/reference	1.61804	0.01
41DAP/reference	0.95992	0.431
42DAP/reference	1.42415	0.046
43DAP/reference	1.28107	0.007
47DAP/reference	1.35278	0.084
52DAP/reference	1.3421	0.013
57DAP/reference	1.57549	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88188	0.268
17DAP/reference	1.01495	0.892
27DAP/reference	1.0133	1
39DAP/reference	1.04713	0.449
41DAP/reference	0.8548	0.014
42DAP/reference	0.86565	0.039
43DAP/reference	1.10689	0.562
47DAP/reference	0.96724	0.319
52DAP/reference	0.88937	0.009
57DAP/reference	1.04738	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80986	0.055
17DAP/reference	0.9365	0.389
27DAP/reference	0.87724	0.038
39DAP/reference	1.01083	0.912
41DAP/reference	0.99502	0.754
42DAP/reference	0.99196	0.816
43DAP/reference	0.84548	0.079
47DAP/reference	0.86262	0.027
52DAP/reference	0.80004	0.144
57DAP/reference	0.90239	0.195

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95	1
26DAP/20DAP	0.96681	1
34DAP/26DAP	0.93636	0.898
51DAP/34DAP	0.63079	0.065
52DAP/51DAP	0.87087	1
53DAP/52DAP	0.88945	0.595
55DAP/53DAP	0.94665	0.725
57DAP/55DAP	1.07497	0.947
62DAP/57DAP	1.4433	0.217
68DAP/62DAP	0.98714	0.834
68DAP/14DAP	1.0408	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.60525	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76211	0.215
Mature Green Tomato/Ripe Tomato	2.6068	0.016
Immature Eggplant/Mature Eggplant	1.92205	0.05
Ripe Pepper/Ripe Tomato	2.02638	1
Mature Eggplant/Ripe Tomato	1.04272	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.72771	0.708
1-1-2/M82	0.68283	1
12-2/M82	N/A	N/A
12-4/M82	1.55092	1
1-3/M82	1.14876
2-1-1/M82	N/A	N/A
2-1/M82	0.76017
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.72597	1
4-1/M82	1.65625
4-3-2/M82	1.415	0.241
4-3/M82	0.76713
5-3/M82	1.33944	0.572
6-2/M82	1.38361	1
6-3/M82	0.64563
7-1/M82	1.32255	0.598
7-2/M82	1.39189	0.385
9-3-2/M82	1.06115

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01727	1
IL2-6/WTpooled	1.37024	0.419
IL7-5/WTpooled	1.29307	0.792
IL7-3/WTpooled	0.93937	0.298
IL12-4/WTpooled	1.16996	0.624
IL1-4/WTpooled	1.09849	1
WT/WTpooled	0.96057	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	1.05282	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9544	1
DC3000/delta hrp 6h	1.10144	1
DC3000/delta hrp 12h	0.93929	1
DC3000/delta hrp 24h	0.73751	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66889
DC3000 delta B/DC3000 delta AB	0.45775	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98117	1
Exp 36h	1.11304	1
Exp 60h	1.03356	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99642	1
Var 0h	1.12822	0.325
Var 12h I row2-row1	0.87436	0.338
Var 12h NI row2-row1	0.95836	0.713
Var 36h I row2-row1	0.82692	1
Var 36h NI row2-row1	1.11256	0.482
Var 60h I row2-row1	1.14852	0.562
Var 60h NI row2-row1	1.03971	1
Time course 0hI-0hNI	0.97195	0.839
Time course 12hI-12hNI	0.99329	1
Time course 36hI-36hNI	0.95346	0.215
Time course 60hI-60hNI	0.37916	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)	0.65413	0.299
transgenic ySAMdc/azygous control (breaker)	1.23723	1
transgenic ySAMdc/azygous control (red)	0.95921	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.28933	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68472	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30268	0.105
Manapal/WT (break)	0.83512	1
Manapal/WT (red)	0.92723	0.607