Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.14.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00827	0.83
27DAP/17DAP	1.61536	0.793
39DAP/27DAP	1.47636	0.944
41DAP/39DAP	0.81228	0.33
42DAP/41DAP	1.44281	0.856
43DAP/42DAP	1.03669	0.937
47DAP/43DAP	1.82768	0.595
52DAP/47DAP	0.98573	0.709
57DAP/52DAP	1.16041	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58671	0.034
17DAP/reference	0.68812	0.021
27DAP/reference	0.67278	0.027
39DAP/reference	0.69504	0.029
41DAP/reference	0.84632	0.085
42DAP/reference	0.85034	0.012
43DAP/reference	0.94984	0.234
47DAP/reference	0.82466	0.001
52DAP/reference	0.69245	0.071
57DAP/reference	0.8188	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75324	0.044
27DAP/17DAP	1.16062	0.848
39DAP/27DAP	1.05564	0.898
41DAP/39DAP	2.36779	0.008
42DAP/41DAP	0.97373	0.746
43DAP/42DAP	0.46886	0.02
47DAP/43DAP	1.28235	0.308
52DAP/47DAP	0.94987	0.839
57DAP/52DAP	1.0256	1
57DAP/7DAP	1.27888	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77084	0.146
17DAP/reference	0.89985	0.019
27DAP/reference	0.96033	0.014
39DAP/reference	0.96702	0.043
41DAP/reference	0.86484	0.037
42DAP/reference	0.88916	0.014
43DAP/reference	0.92373	0.072
47DAP/reference	0.74148	0.128
52DAP/reference	0.89482	0.106
57DAP/reference	0.91905	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74421	0.045
17DAP/reference	0.67022	0.009
27DAP/reference	0.83298	0.134
39DAP/reference	0.7095	0.047
41DAP/reference	0.72884	0.046
42DAP/reference	0.78579	0.037
43DAP/reference	1.09243	0.929
47DAP/reference	0.8327	0.055
52DAP/reference	0.60325	0.006
57DAP/reference	0.87615	0.116

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8847	0.147
17DAP/reference	0.84065	0.177
27DAP/reference	0.90233	0.206
39DAP/reference	0.86253	0.101
41DAP/reference	0.92598	0.167
42DAP/reference	0.93003	0.445
43DAP/reference	0.88297	0.15
47DAP/reference	0.63072	0.004
52DAP/reference	0.75588	0.125
57DAP/reference	0.70505	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87851	0.915
26DAP/20DAP	0.63052	0.512
34DAP/26DAP	1.72464	0.819
51DAP/34DAP	0.76047
52DAP/51DAP	1.52024	0.492
53DAP/52DAP	0.82868	0.572
55DAP/53DAP	1.40867	0.053
57DAP/55DAP	0.76486	0.194
62DAP/57DAP	1.04098	1
68DAP/62DAP	0.65764	0.135
68DAP/14DAP	0.73907	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83976	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.21213	0.06
Mature Green Tomato/Ripe Tomato	1.52288	0.881
Immature Eggplant/Mature Eggplant	3.36041	0.05
Ripe Pepper/Ripe Tomato	4.37633	0.258
Mature Eggplant/Ripe Tomato	0.9468	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.59251	0.613
1-1-2/M82	0.93897	1
12-2/M82	1.0157	1
12-4/M82	1.50438	1
1-3/M82	1.60039
2-1-1/M82	1.02058	1
2-1/M82	N/A	N/A
2-6/M82	0.72892
3-2/M82	1.80604
4-1-1/M82	1.2093	1
4-1/M82	1.45053	0.853
4-3-2/M82	2.05436
4-3/M82	0.77366	0.578
5-3/M82	1.77845	0.572
6-2/M82	4.09194	0.235
6-3/M82	0.96429	1
7-1/M82	1.06541	1
7-2/M82	1.20974	0.385
9-3-2/M82	0.87795

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.20447	0.277
IL2-6/WTpooled	1.0587	0.441
IL7-5/WTpooled	1.17292	0.792
IL7-3/WTpooled	0.96155	1
IL12-4/WTpooled	1.13025	0.673
IL1-4/WTpooled	1.14413	0.426
WT/WTpooled	0.98728	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	1.25281	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00484	1
DC3000/delta hrp 6h	1.01614	0.95
DC3000/delta hrp 12h	1.07532	1
DC3000/delta hrp 24h	1.7566	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.82927
DC3000 delta B/DC3000 delta AB	3.98603	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.81239	1
Exp 36h	2.04795	0.409
Exp 60h	2.89874	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95724	1
Var 0h	0.49501	1
Var 12h I row2-row1	1.04633	0.736
Var 12h NI row2-row1	1.9815	0.649
Var 36h I row2-row1	1.31323	1
Var 36h NI row2-row1	0.60445	0.522
Var 60h I row2-row1	0.81354	0.293
Var 60h NI row2-row1	0.65394	0.292
Time course 0hI-0hNI	1.57848	0.323
Time course 12hI-12hNI	1.1598	0.762
Time course 36hI-36hNI	3.67113	0.004
Time course 60hI-60hNI	60.8332	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)	1.21001	0.654
transgenic ySAMdc/azygous control (breaker)	0.99123	1
transgenic ySAMdc/azygous control (red)	0.96638	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98908	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.77265	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.71113	0.307
Manapal/WT (break)	1.73116	1
Manapal/WT (red)	0.76839	0.36