Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45407	0.428
27DAP/17DAP	1.03067	0.959
39DAP/27DAP	1.76425	0.095
41DAP/39DAP	1.12971	0.871
42DAP/41DAP	1.31791	0.844
43DAP/42DAP	1.7029	0.095
47DAP/43DAP	0.77389	0.345
52DAP/47DAP	1.15888	0.907
57DAP/52DAP	1.17487	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00961	0.63
17DAP/reference	1.19301	0.108
27DAP/reference	1.17811	0.314
39DAP/reference	1.11285	0.343
41DAP/reference	1.20951	0.015
42DAP/reference	1.22947	0.01
43DAP/reference	1.16969	0.047
47DAP/reference	1.28039	0.008
52DAP/reference	1.278	0.059
57DAP/reference	0.92723	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96597	0.629
27DAP/17DAP	1.43704	0.32
39DAP/27DAP	1.22508	0.32
41DAP/39DAP	1.49236	0.163
42DAP/41DAP	1.15864	0.47
43DAP/42DAP	1.15681	0.324
47DAP/43DAP	0.98879	0.947
52DAP/47DAP	1.32966	0.296
57DAP/52DAP	1.18109	0.378
57DAP/7DAP	1.11738	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95538	0.613
17DAP/reference	0.66253	0.039
27DAP/reference	0.71772	0.018
39DAP/reference	0.85662	0.083
41DAP/reference	0.8053	0.127
42DAP/reference	0.78198	0.082
43DAP/reference	0.8723	0.183
47DAP/reference	1.08288	0.915
52DAP/reference	0.82388	0.213
57DAP/reference	0.84765	0.059

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6338	0.012
17DAP/reference	0.82304	0.063
27DAP/reference	0.9379	0.381
39DAP/reference	1.10336	0.912
41DAP/reference	1.28438	0.146
42DAP/reference	1.04791	1
43DAP/reference	0.9032	0.166
47DAP/reference	1.19807	0.225
52DAP/reference	1.28834	0.279
57DAP/reference	1.02439	0.827

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96727	0.391
17DAP/reference	0.89659	0.389
27DAP/reference	1.2853	0.325
39DAP/reference	0.91431	0.222
41DAP/reference	0.93873	0.512
42DAP/reference	0.99431	0.816
43DAP/reference	1.29547	0.209
47DAP/reference	1.327	0.294
52DAP/reference	0.85796	0.256
57DAP/reference	1.32599	0.126

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24805	0.966
26DAP/20DAP	1.31887	0.567
34DAP/26DAP	0.87039	0.841
51DAP/34DAP	0.56266
52DAP/51DAP	0.78258	1
53DAP/52DAP	1.04343	0.929
55DAP/53DAP	1.21794	0.981
57DAP/55DAP	1.20802	0.87
62DAP/57DAP	1.0459	1
68DAP/62DAP	1.46952	0.885
68DAP/14DAP	0.81507

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.55257	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.25432	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.64843
Mature Eggplant/Ripe Tomato	0.53182	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.53976	0.742
1-1-2/M82	0.9805	1
12-2/M82	0.75893
12-4/M82	0.94606	1
1-3/M82	1.96755	1
2-1-1/M82	1.3914	0.457
2-1/M82	0.71335	0.519
2-6/M82	0.80134	1
3-2/M82	1.7385
4-1-1/M82	1.03829	1
4-1/M82	0.4448
4-3-2/M82	0.80124
4-3/M82	0.98617	1
5-3/M82	0.92514	0.642
6-2/M82	2.27755
6-3/M82	0.63944	0.982
7-1/M82	N/A	N/A
7-2/M82	1.0677	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99715	1
IL7-5/WTpooled	0.62163	0.559
IL7-3/WTpooled	0.69631	0.298
IL12-4/WTpooled	0.71236	0.581
IL1-4/WTpooled	0.95402	1
WT/WTpooled	1.02492	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	1.05972	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03594	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.05027	1
DC3000/delta hrp 24h	2.65008	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96992	1
DC3000 delta B/DC3000 delta AB	1.00116	0.693

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	0.99463	1
Var 0h	1.23512	0.936
Var 12h I row2-row1	0.95054	0.77
Var 12h NI row2-row1	0.97847	0.713
Var 36h I row2-row1	1.12868	0.489
Var 36h NI row2-row1	0.96314	0.743
Var 60h I row2-row1	0.91404	0.582
Var 60h NI row2-row1	0.98309	1
Time course 0hI-0hNI	1.01516	0.852
Time course 12hI-12hNI	1.01132	0.868
Time course 36hI-36hNI	1.17574	0.011
Time course 60hI-60hNI	1.35774	0.06

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)	1.19594	1
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.6578	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.34715	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.26249	0.381
Manapal/WT (red)	0.91519	0.503