Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97771	0.811
27DAP/17DAP	0.97676	0.894
39DAP/27DAP	1.2135	0.638
41DAP/39DAP	0.94888	0.756
42DAP/41DAP	1.02217	1
43DAP/42DAP	1.05215	1
47DAP/43DAP	1.01077	1
52DAP/47DAP	0.81604	0.539
57DAP/52DAP	1.09123	0.944

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.72759	0.007
17DAP/reference	1.19958	0.21
27DAP/reference	0.97847	0.654
39DAP/reference	1.14944	1
41DAP/reference	1.08246	0.587
42DAP/reference	1.70991	0.001
43DAP/reference	1.61892	0.007
47DAP/reference	1.72118	0.001
52DAP/reference	1.07326	0.32
57DAP/reference	1.27409	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92923	0.496
27DAP/17DAP	1.08404	0.9
39DAP/27DAP	0.8295	0.056
41DAP/39DAP	1.13399	0.79
42DAP/41DAP	1.00697	0.825
43DAP/42DAP	1.04755	0.554
47DAP/43DAP	0.93757	0.656
52DAP/47DAP	0.9152	0.35
57DAP/52DAP	0.88261	0.407
57DAP/7DAP	0.60113	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35711	0.046
17DAP/reference	1.39319	0.022
27DAP/reference	1.17316	0.026
39DAP/reference	1.29214	0.01
41DAP/reference	1.12054	0.475
42DAP/reference	1.40689	0.024
43DAP/reference	1.24355	0.02
47DAP/reference	1.30552	0.02
52DAP/reference	1.25636	0.043
57DAP/reference	1.13001	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48488	0.042
17DAP/reference	1.97043	0.008
27DAP/reference	1.78594	0.013
39DAP/reference	1.10667	0.346
41DAP/reference	1.08197	0.72
42DAP/reference	1.48562	0.022
43DAP/reference	1.46805	0.103
47DAP/reference	1.48764	0.015
52DAP/reference	0.9031	0.111
57DAP/reference	1.04422	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2771	0.023
17DAP/reference	1.41149	0.077
27DAP/reference	1.16236	0.048
39DAP/reference	1.43937	0.005
41DAP/reference	1.19126	0.089
42DAP/reference	1.67315	0.018
43DAP/reference	2.018	0.012
47DAP/reference	1.59851	0.007
52DAP/reference	1.52759	0.087
57DAP/reference	1.48422	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85719	1
26DAP/20DAP	1.60329	0.099
34DAP/26DAP	1.27377	1
51DAP/34DAP	1.64746	0.039
52DAP/51DAP	0.63711	0.151
53DAP/52DAP	1.24472	0.428
55DAP/53DAP	0.63823	0.022
57DAP/55DAP	1.44003	0.185
62DAP/57DAP	1.00476	1
68DAP/62DAP	1.65746	0.087
68DAP/14DAP	4.00905	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86958	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.65489	0.167
Mature Green Tomato/Ripe Tomato	0.90309	0.487
Immature Eggplant/Mature Eggplant	1.60686	0.05
Ripe Pepper/Ripe Tomato	4.27891	0.256
Mature Eggplant/Ripe Tomato	1.78644	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28359	0.536
1-1-2/M82	1.10109	1
12-2/M82	0.85274	0.955
12-4/M82	1.02301	1
1-3/M82	1.32182	1
2-1-1/M82	0.82614	0.784
2-1/M82	0.69381
2-6/M82	1.03068	1
3-2/M82	1.22809	0.967
4-1-1/M82	1.12443	1
4-1/M82	3.28946	0.512
4-3-2/M82	1.31746	0.253
4-3/M82	1.55585	0.268
5-3/M82	1.20632	0.572
6-2/M82	1.29142
6-3/M82	0.75014	0.982
7-1/M82	0.91426
7-2/M82	1.21009
9-3-2/M82	1.27489	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73011	0.243
IL2-6/WTpooled	0.89409	0.473
IL7-5/WTpooled	1.11078	0.792
IL7-3/WTpooled	0.75986	0.31
IL12-4/WTpooled	0.88429	0.581
IL1-4/WTpooled	0.93001	0.699
WT/WTpooled	0.92669	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	1.05936	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05485	0.921
DC3000/delta hrp 6h	0.93173	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.96103	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97628
DC3000 delta B/DC3000 delta AB	0.76853	0.326

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00036	1
Exp 36h	0.78356	0.749
Exp 60h	0.78873	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00283	1
Var 0h	0.5535	1
Var 12h I row2-row1	0.87494	0.418
Var 12h NI row2-row1	1.05366	1
Var 36h I row2-row1	0.93028	0.805
Var 36h NI row2-row1	1.13533	1
Var 60h I row2-row1	0.84272	0.374
Var 60h NI row2-row1	0.89632	0.483
Time course 0hI-0hNI	0.93172	0.408
Time course 12hI-12hNI	1.02427	0.754
Time course 36hI-36hNI	1.00529	1
Time course 60hI-60hNI	0.94719	0.646

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)	1.14273	0.325
transgenic ySAMdc/azygous control (breaker)	1.76902	0.165
transgenic ySAMdc/azygous control (red)	1.20296	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.983	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19051	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.57437	0.084
Manapal/WT (break)	1.29453	0.183
Manapal/WT (red)	1.99655	0.133