Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09933	0.709
27DAP/17DAP	1.23475	0.829
39DAP/27DAP	1.1621	0.845
41DAP/39DAP	0.70123	0.133
42DAP/41DAP	1.33265	0.199
43DAP/42DAP	0.87003	0.613
47DAP/43DAP	1.13222	0.793
52DAP/47DAP	2.04899	0.236
57DAP/52DAP	0.65356	0.577

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83487	0.159
17DAP/reference	0.75808	0.007
27DAP/reference	0.94866	0.525
39DAP/reference	0.78076	0.016
41DAP/reference	0.73255	0.009
42DAP/reference	0.86362	0.006
43DAP/reference	0.95549	0.36
47DAP/reference	1.0857	0.794
52DAP/reference	1.39477	0.008
57DAP/reference	1.24102	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1742	0.074
27DAP/17DAP	1.0027	0.969
39DAP/27DAP	0.89843	0.601
41DAP/39DAP	1.32622	0.304
42DAP/41DAP	0.89593	0.329
43DAP/42DAP	0.91281	0.447
47DAP/43DAP	1.08795	0.827
52DAP/47DAP	1.17378	0.512
57DAP/52DAP	1.97551	0.029
57DAP/7DAP	1.82522	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12449	0.501
17DAP/reference	1.21275	0.134
27DAP/reference	1.13406	0.131
39DAP/reference	1.18476	0.09
41DAP/reference	1.20118	0.075
42DAP/reference	1.05234	0.686
43DAP/reference	0.93259	0.279
47DAP/reference	1.16122	0.096
52DAP/reference	1.18106	0.121
57DAP/reference	1.2678	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67729	0.006
17DAP/reference	0.61756	0.005
27DAP/reference	0.83418	0.081
39DAP/reference	0.88074	0.077
41DAP/reference	1.09343	0.629
42DAP/reference	0.87527	0.067
43DAP/reference	0.7196	0.082
47DAP/reference	0.84424	0.011
52DAP/reference	0.86284	0.01
57DAP/reference	0.67593	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12611	0.588
17DAP/reference	0.97407	0.658
27DAP/reference	1.30152	0.227
39DAP/reference	1.15933	0.451
41DAP/reference	1.08789	0.357
42DAP/reference	1.15881	0.106
43DAP/reference	1.15031	0.27
47DAP/reference	1.02105	0.731
52DAP/reference	1.24302	0.161
57DAP/reference	1.79307	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11627	0.966
26DAP/20DAP	1.44934	0.132
34DAP/26DAP	0.90647	0.735
51DAP/34DAP	1.321	0.084
52DAP/51DAP	0.81612	1
53DAP/52DAP	0.93821	0.79
55DAP/53DAP	0.90824	0.563
57DAP/55DAP	1.17603	0.927
62DAP/57DAP	0.98303	1
68DAP/62DAP	1.82458	0.353
68DAP/14DAP	3.16838	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99131	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.53426	0.121
Mature Green Tomato/Ripe Tomato	0.36343	0.021
Immature Eggplant/Mature Eggplant	0.77581	0.092
Ripe Pepper/Ripe Tomato	0.36981	0.224
Mature Eggplant/Ripe Tomato	0.36605	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02858
1-1-2/M82	1.16074	1
12-2/M82	N/A	N/A
12-4/M82	0.77096
1-3/M82	N/A	N/A
2-1-1/M82	0.60232
2-1/M82	N/A	N/A
2-6/M82	1.23896	0.505
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.0581
5-3/M82	1.06483	1
6-2/M82	1.47809
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.24865
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17489	0.277
IL2-6/WTpooled	1.04967	1
IL7-5/WTpooled	0.71112
IL7-3/WTpooled	1.1608	1
IL12-4/WTpooled	1.05912	0.673
IL1-4/WTpooled	1.03902	1
WT/WTpooled	0.95434	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	1.00661	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08594	0.921
DC3000/delta hrp 6h	1.01874	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.92006	0.455

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14782	0.102
DC3000 delta B/DC3000 delta AB	0.93378	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13248	1
Exp 36h	1.02464	1
Exp 60h	0.98399	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.34345	1
Var 12h I row2-row1	0.97788	0.948
Var 12h NI row2-row1	0.97067	0.906
Var 36h I row2-row1	1.10375	1
Var 36h NI row2-row1	1.02301	1
Var 60h I row2-row1	0.98094	0.952
Var 60h NI row2-row1	0.88811	0.756
Time course 0hI-0hNI	0.99967	1
Time course 12hI-12hNI	0.97828	0.909
Time course 36hI-36hNI	1.1278	0.114
Time course 60hI-60hNI	1.07405	0.115

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)	1.13459	0.541
transgenic ySAMdc/azygous control (breaker)	0.56307	0.137
transgenic ySAMdc/azygous control (red)	1.06553	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09576	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.76388	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87934	1
Manapal/WT (break)	1.08706	1
Manapal/WT (red)	1.18519	0.222