Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.54849	0.244
27DAP/17DAP	1.49908	0.693
39DAP/27DAP	1.43499	0.745
41DAP/39DAP	1.31491	0.597
42DAP/41DAP	1.20076	0.937
43DAP/42DAP	1.2348	0.956
47DAP/43DAP	1.4004	0.776
52DAP/47DAP	0.85825	0.595
57DAP/52DAP	1.22905	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11081	0.265
17DAP/reference	1.4137	0.08
27DAP/reference	1.44735	0.146
39DAP/reference	1.73115	0.122
41DAP/reference	1.97119	0.012
42DAP/reference	3.66813
43DAP/reference	2.99534
47DAP/reference	N/A	N/A
52DAP/reference	1.20284	0.515
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85354	0.087
27DAP/17DAP	1.064	0.775
39DAP/27DAP	1.08409	0.519
41DAP/39DAP	0.98005	0.973
42DAP/41DAP	1.04393	0.593
43DAP/42DAP	1.136	0.049
47DAP/43DAP	0.99772	0.997
52DAP/47DAP	0.98719	0.93
57DAP/52DAP	0.89303	0.328
57DAP/7DAP	0.92393	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84549	0.063
17DAP/reference	0.88983	0.011
27DAP/reference	0.87128	0.011
39DAP/reference	0.8966	0.012
41DAP/reference	1.11543	0.812
42DAP/reference	0.84188	0.01
43DAP/reference	0.87823	0.028
47DAP/reference	1.59134	0.149
52DAP/reference	0.83852	0.022
57DAP/reference	0.87848	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14524	0.507
17DAP/reference	1.30849	0.068
27DAP/reference	1.24424	0.297
39DAP/reference	1.17685	0.62
41DAP/reference	1.34395	0.157
42DAP/reference	1.1653	1
43DAP/reference	1.23046	0.268
47DAP/reference	0.88198	0.41
52DAP/reference	0.93608	0.302
57DAP/reference	1.31601	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93969	0.311
17DAP/reference	0.96103	0.579
27DAP/reference	0.8711	0.033
39DAP/reference	0.85955	0.035
41DAP/reference	0.96509	0.209
42DAP/reference	0.98877	0.816
43DAP/reference	1.5122	0.168
47DAP/reference	2.20654	0.018
52DAP/reference	1.42775	0.457
57DAP/reference	1.49162	0.285

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01201	1
26DAP/20DAP	0.92415	0.512
34DAP/26DAP	1.04752	1
51DAP/34DAP	1.0933	0.271
52DAP/51DAP	1.01553	0.873
53DAP/52DAP	1.02925	0.91
55DAP/53DAP	1.02983	0.927
57DAP/55DAP	1.09909	0.643
62DAP/57DAP	0.88692	0.28
68DAP/62DAP	0.96667	0.81
68DAP/14DAP	0.68905	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15859	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.85814	0.287
Immature Eggplant/Mature Eggplant	2.05654
Ripe Pepper/Ripe Tomato	0.11168	0.224
Mature Eggplant/Ripe Tomato	0.03508	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06861	1
1-1-2/M82	0.97356	1
12-2/M82	1.0091	1
12-4/M82	0.96981	0.33
1-3/M82	2.17111	0.248
2-1-1/M82	0.8254	0.465
2-1/M82	1.01395	1
2-6/M82	0.90143	1
3-2/M82	1.07743	0.84
4-1-1/M82	0.86755	1
4-1/M82	1.09061
4-3-2/M82	1.10574	1
4-3/M82	0.91572	0.72
5-3/M82	0.92565	1
6-2/M82	1.01997	1
6-3/M82	0.94464	1
7-1/M82	0.99231	1
7-2/M82	1.00977	1
9-3-2/M82	0.80462	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81117
IL2-6/WTpooled	1.08613
IL7-5/WTpooled	1.69727	0.75
IL7-3/WTpooled	2.15764	1
IL12-4/WTpooled	1.16435	0.839
IL1-4/WTpooled	1.43357	0.426
WT/WTpooled	1.00385	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	1.3037	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06287	0.875
DC3000/delta hrp 6h	1.0005	0.95
DC3000/delta hrp 12h	0.98145	1
DC3000/delta hrp 24h	0.52189	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23183	0.16
DC3000 delta B/DC3000 delta AB	1.18536	0.304

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98974	1
Var 0h	0.55397	0.98
Var 12h I row2-row1	0.96675	0.705
Var 12h NI row2-row1	0.9587	0.82
Var 36h I row2-row1	1.26937	0.908
Var 36h NI row2-row1	0.79873	0.61
Var 60h I row2-row1	0.96022	0.285
Var 60h NI row2-row1	1.08431	0.904
Time course 0hI-0hNI	1.03307	1
Time course 12hI-12hNI	1.02267	0.816
Time course 36hI-36hNI	1.04706	0.975
Time course 60hI-60hNI	1.58622	0.009

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)	0.43621	0.246
transgenic ySAMdc/azygous control (breaker)	1.16033	1
transgenic ySAMdc/azygous control (red)	1.20694	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.21792	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.72476	0.096
Manapal/WT (break)	1.35515	0.123
Manapal/WT (red)	0.84267	0.36