Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.19.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11198	0.997
27DAP/17DAP	1.12514	0.854
39DAP/27DAP	3.76621	0.021
41DAP/39DAP	1.06708	0.67
42DAP/41DAP	1.17657	0.912
43DAP/42DAP	1.42715	0.512
47DAP/43DAP	1.64658	0.216
52DAP/47DAP	1.02538	0.884
57DAP/52DAP	2.48877	0.524

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62879	0.034
17DAP/reference	0.61405	0.009
27DAP/reference	0.68233	0.024
39DAP/reference	0.84054	0.284
41DAP/reference	0.65604	0.009
42DAP/reference	1.13531	0.089
43DAP/reference	0.99755	0.904
47DAP/reference	1.79677	0.001
52DAP/reference	1.45719	0.008
57DAP/reference	1.49462	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24771	0.719
27DAP/17DAP	1.59637	0.036
39DAP/27DAP	1.72404	0.314
41DAP/39DAP	0.62105	0.09
42DAP/41DAP	0.95705	0.753
43DAP/42DAP	1.08943	0.478
47DAP/43DAP	1.50029	0.026
52DAP/47DAP	1.06558	0.941
57DAP/52DAP	1.78417	0.082
57DAP/7DAP	2.04975	0.132

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78362	0.088
17DAP/reference	0.87554	0.144
27DAP/reference	1.01805	0.974
39DAP/reference	1.31111	0.282
41DAP/reference	1.75907	0.008
42DAP/reference	1.73802	0.01
43DAP/reference	1.42858	0.027
47DAP/reference	1.27978	0.05
52DAP/reference	1.75471	0.025
57DAP/reference	3.28996	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.46637	0.006
17DAP/reference	0.46124	0.003
27DAP/reference	0.83364	0.123
39DAP/reference	0.87434	0.083
41DAP/reference	1.08216	0.262
42DAP/reference	1.0435	0.879
43DAP/reference	0.79487	0.082
47DAP/reference	2.48073	0.008
52DAP/reference	1.00102	0.761
57DAP/reference	1.04861	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81279	0.052
17DAP/reference	0.77772	0.162
27DAP/reference	1.42533	0.156
39DAP/reference	1.39232	0.015
41DAP/reference	1.34137	0.011
42DAP/reference	1.56492	0.017
43DAP/reference	1.52706	0.008
47DAP/reference	2.27923	0.006
52DAP/reference	2.53289	0.027
57DAP/reference	2.06941	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21537	0.966
26DAP/20DAP	1.79346	0.285
34DAP/26DAP	0.94494	0.909
51DAP/34DAP	3.29726	0.023
52DAP/51DAP	0.71769	1
53DAP/52DAP	1.63539	0.037
55DAP/53DAP	0.4971	0.018
57DAP/55DAP	1.03413	0.925
62DAP/57DAP	3.32832	0.024
68DAP/62DAP	1.67458	0.121
68DAP/14DAP	4.401	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98185	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.03181	0.039
Mature Green Tomato/Ripe Tomato	0.24746	0.016
Immature Eggplant/Mature Eggplant	28.324	0.042
Ripe Pepper/Ripe Tomato	1.57384	1
Mature Eggplant/Ripe Tomato	0.40976	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.84175	0.557
1-1-2/M82	1.47399	1
12-2/M82	1.15648	1
12-4/M82	1.13187	1
1-3/M82	3.32987	0.277
2-1-1/M82	0.93089	0.784
2-1/M82	1.02279	1
2-6/M82	1.32237	0.405
3-2/M82	1.1962	0.717
4-1-1/M82	1.29033	1
4-1/M82	1.88	1
4-3-2/M82	2.17147	0.284
4-3/M82	1.12762	1
5-3/M82	0.43036	0.49
6-2/M82	0.65458	0.481
6-3/M82	1.11102	1
7-1/M82	0.99002	1
7-2/M82	2.74589	0.318
9-3-2/M82	2.56157	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.74756	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.66452
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.59668	0.581
IL1-4/WTpooled	0.82554	0.457
WT/WTpooled	1.00231	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	1.49201	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.96453	0.95
DC3000/delta hrp 12h	1.0984	1
DC3000/delta hrp 24h	1.09351	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	5.08283	0.061

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19948	1
Exp 36h	1.10643	1
Exp 60h	1.11361	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02508	1
Var 0h	0.98159	1
Var 12h I row2-row1	0.89719	0.77
Var 12h NI row2-row1	1.7655	0.34
Var 36h I row2-row1	1.14852	0.908
Var 36h NI row2-row1	0.79883	0.645
Var 60h I row2-row1	0.46756	0.285
Var 60h NI row2-row1	0.5569	0.298
Time course 0hI-0hNI	1.22263	0.344
Time course 12hI-12hNI	1.65075	0.056
Time course 36hI-36hNI	4.51738	0.005
Time course 60hI-60hNI	20.6717	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)	0.6069	0.314
transgenic ySAMdc/azygous control (breaker)	0.98343	1
transgenic ySAMdc/azygous control (red)	1.1087	0.92

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	0.72693	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.76365	0.093
Manapal/WT (break)	3.7165	0.183
Manapal/WT (red)	1.26051	0.164