Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.8.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.71495	0.056
27DAP/17DAP	1.37725	0.699
39DAP/27DAP	2.16788	0.058
41DAP/39DAP	1.04912	0.992
42DAP/41DAP	1.50612	0.089
43DAP/42DAP	0.91848	0.851
47DAP/43DAP	0.76521	0.314
52DAP/47DAP	0.66694	0.246
57DAP/52DAP	1.2408	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56354	0.027
17DAP/reference	1.38534	0.201
27DAP/reference	1.7539	0.009
39DAP/reference	1.14564	0.403
41DAP/reference	1.22605	0.026
42DAP/reference	1.39366	0.01
43DAP/reference	1.22795	0.074
47DAP/reference	1.45796	0.057
52DAP/reference	1.5427	0.041
57DAP/reference	1.52805	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.88478	0.036
27DAP/17DAP	0.77193	0.446
39DAP/27DAP	1.76954	0.07
41DAP/39DAP	0.91206	0.495
42DAP/41DAP	1.3807	0.139
43DAP/42DAP	1.28653	0.25
47DAP/43DAP	0.90326	0.41
52DAP/47DAP	0.92192	0.729
57DAP/52DAP	0.70886	0.125
57DAP/7DAP	2.16296	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91322	0.27
17DAP/reference	0.72423	0.014
27DAP/reference	0.79375	0.016
39DAP/reference	1.64674	0.007
41DAP/reference	0.84425	0.174
42DAP/reference	1.03429	0.889
43DAP/reference	1.43052	0.01
47DAP/reference	2.24447	0.014
52DAP/reference	1.68508	0.007
57DAP/reference	2.46281	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51456	0.007
17DAP/reference	0.84041	0.041
27DAP/reference	0.96588	0.467
39DAP/reference	1.30875	0.032
41DAP/reference	0.98156	0.481
42DAP/reference	1.16083	0.317
43DAP/reference	1.1599	0.411
47DAP/reference	1.73711	0.011
52DAP/reference	0.90697	0.101
57DAP/reference	1.16162	0.296

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.52646	0.02
17DAP/reference	0.7159	0.107
27DAP/reference	0.65347	0.033
39DAP/reference	0.86254	0.026
41DAP/reference	0.90896	0.119
42DAP/reference	1.22982	0.103
43DAP/reference	0.97575	0.568
47DAP/reference	0.59492	0.006
52DAP/reference	0.66205	0.169
57DAP/reference	1.22277	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90445	0.89
26DAP/20DAP	0.74205	0.512
34DAP/26DAP	0.82508	0.093
51DAP/34DAP	1.52932	0.055
52DAP/51DAP	0.63116	0.079
53DAP/52DAP	1.31288	0.06
55DAP/53DAP	0.34133	0.016
57DAP/55DAP	0.89166	0.606
62DAP/57DAP	5.46664	0.002
68DAP/62DAP	1.70309	0.589
68DAP/14DAP	1.19907	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.89326	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50611	0.131
Mature Green Tomato/Ripe Tomato	2.01645	0.363
Immature Eggplant/Mature Eggplant	2.19366	0.05
Ripe Pepper/Ripe Tomato	1.68159	1
Mature Eggplant/Ripe Tomato	1.58618	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05542	0.877
1-1-2/M82	1.1183	1
12-2/M82	1.28057	1
12-4/M82	1.21185	1
1-3/M82	1.53137	0.255
2-1-1/M82	0.84011	0.465
2-1/M82	0.92653	0.74
2-6/M82	0.998	1
3-2/M82	1.11088	0.84
4-1-1/M82	0.98242	1
4-1/M82	1.36974	0.853
4-3-2/M82	1.33333	0.508
4-3/M82	0.94054	1
5-3/M82	0.99706	1
6-2/M82	1.01991	1
6-3/M82	0.98286	1
7-1/M82	0.98452	1
7-2/M82	0.90898	0.57
9-3-2/M82	1.13165	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.50961
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.71244	0.418
IL12-4/WTpooled	1.0316	1
IL1-4/WTpooled	1.39628	0.426
WT/WTpooled	1.02433	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	1.6008	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06582	0.921
DC3000/delta hrp 6h	1.11694	1
DC3000/delta hrp 12h	1.4035	1
DC3000/delta hrp 24h	0.96101	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82716	0.059
DC3000 delta B/DC3000 delta AB	1.1781	0.363

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04678	1
Exp 36h	1.81617	0.693
Exp 60h	1.78407	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04278	1
Var 0h	1.1142	0.98
Var 12h I row2-row1	1.16067	0.692
Var 12h NI row2-row1	1.39938	0.266
Var 36h I row2-row1	1.30135	0.309
Var 36h NI row2-row1	0.72246	0.478
Var 60h I row2-row1	0.54808	0.285
Var 60h NI row2-row1	0.84924	0.756
Time course 0hI-0hNI	1.33828	0.377
Time course 12hI-12hNI	1.06093	0.747
Time course 36hI-36hNI	1.44222	0.011
Time course 60hI-60hNI	6.87041	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)	0.89034	0.314
transgenic ySAMdc/azygous control (breaker)	1.12444	0.178
transgenic ySAMdc/azygous control (red)	1.09136	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.35157	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55734	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16413	0.307
Manapal/WT (break)	1.10098	0.183
Manapal/WT (red)	0.85571	0.424