Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90829	0.543
27DAP/17DAP	0.89806	0.754
39DAP/27DAP	2.21425	0.052
41DAP/39DAP	0.66609	0.086
42DAP/41DAP	1.1465	0.978
43DAP/42DAP	1.16147	1
47DAP/43DAP	0.77983	0.366
52DAP/47DAP	1.28998	0.847
57DAP/52DAP	1.46797	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30877	0.016
17DAP/reference	0.89389	0.208
27DAP/reference	0.96503	0.595
39DAP/reference	0.97076	0.663
41DAP/reference	0.84955	0.085
42DAP/reference	1.19916	0.008
43DAP/reference	1.04494	0.617
47DAP/reference	1.49829	0.001
52DAP/reference	1.68556	0.008
57DAP/reference	1.67254	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3824	0.065
27DAP/17DAP	1.08111	0.754
39DAP/27DAP	1.0217	1
41DAP/39DAP	1.07538	1
42DAP/41DAP	1.09311	0.935
43DAP/42DAP	0.84662	0.079
47DAP/43DAP	0.9841	0.911
52DAP/47DAP	1.0308	0.979
57DAP/52DAP	1.12292	0.355
57DAP/7DAP	1.21844	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89139	0.024
17DAP/reference	1.31867	0.009
27DAP/reference	1.32149	0.009
39DAP/reference	1.48391	0.006
41DAP/reference	1.33287	0.023
42DAP/reference	1.66025	0.011
43DAP/reference	1.52066	0.009
47DAP/reference	1.87887	0.014
52DAP/reference	1.66992	0.009
57DAP/reference	1.4044	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93279	0.374
17DAP/reference	0.98358	0.611
27DAP/reference	1.22399	0.195
39DAP/reference	1.18784	0.233
41DAP/reference	0.91945	0.169
42DAP/reference	1.19438	0.126
43DAP/reference	0.8307	0.135
47DAP/reference	1.20875	0.076
52DAP/reference	0.67389	0.004
57DAP/reference	0.85226	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35903	0.106
17DAP/reference	0.9374	0.462
27DAP/reference	1.16827	0.1
39DAP/reference	1.46285	0.025
41DAP/reference	1.19011	0.022
42DAP/reference	1.49083	0.021
43DAP/reference	1.55784	0.019
47DAP/reference	1.02217	0.708
52DAP/reference	1.66479	0.036
57DAP/reference	3.83399	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85793	0.281
26DAP/20DAP	1.58594	0.103
34DAP/26DAP	0.9355	0.741
51DAP/34DAP	1.67983	0.031
52DAP/51DAP	0.84796	1
53DAP/52DAP	1.51054	0.044
55DAP/53DAP	0.66966	0.064
57DAP/55DAP	1.02565	0.93
62DAP/57DAP	0.69292	0.007
68DAP/62DAP	1.10066	0.747
68DAP/14DAP	1.30345	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23724	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81733	0.274
Mature Green Tomato/Ripe Tomato	1.3859	0.119
Immature Eggplant/Mature Eggplant	1.34973	0.05
Ripe Pepper/Ripe Tomato	1.03957	1
Mature Eggplant/Ripe Tomato	1.35707	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.20801	1
1-3/M82	N/A	N/A
2-1-1/M82	1.03256
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.02397	1
4-1-1/M82	N/A	N/A
4-1/M82	2.46943
4-3-2/M82	0.81316
4-3/M82	0.96804
5-3/M82	1.13176	0.455
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.81861
9-3-2/M82	1.15245	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90973	1
IL2-6/WTpooled	1.19861	0.427
IL7-5/WTpooled	0.98856
IL7-3/WTpooled	0.85065	0.418
IL12-4/WTpooled	0.97241	1
IL1-4/WTpooled	0.92672	0.834
WT/WTpooled	1.00352	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	1.15734	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07444	0.894
DC3000/delta hrp 6h	0.96608	0.95
DC3000/delta hrp 12h	1.02577	1
DC3000/delta hrp 24h	1.03937	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1924	0.045
DC3000 delta B/DC3000 delta AB	1.34552	0.112

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19779	1
Exp 36h	1.29828	0.693
Exp 60h	1.53268	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00181	1
Var 0h	1.01997	1
Var 12h I row2-row1	0.95295	0.856
Var 12h NI row2-row1	1.14905	0.649
Var 36h I row2-row1	1.18709	0.41
Var 36h NI row2-row1	0.99787	1
Var 60h I row2-row1	0.70393	0.293
Var 60h NI row2-row1	0.94694	1
Time course 0hI-0hNI	0.99621	1
Time course 12hI-12hNI	1.08727	0.293
Time course 36hI-36hNI	1.38015	0.006
Time course 60hI-60hNI	1.68667	0.008

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)	0.97293	0.722
transgenic ySAMdc/azygous control (breaker)	1.14275	1
transgenic ySAMdc/azygous control (red)	1.06518	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02689	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83109	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91404	1
Manapal/WT (break)	1.00292	1
Manapal/WT (red)	1.01097	1