Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28786	0.798
27DAP/17DAP	1.92211	0.243
39DAP/27DAP	6.94497	0.02
41DAP/39DAP	2.5183	0.225
42DAP/41DAP	3.86669	0.025
43DAP/42DAP	1.54246	1
47DAP/43DAP	1.04742	0.884
52DAP/47DAP	0.65231	0.241
57DAP/52DAP	1.81581	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.44457	0.025
17DAP/reference	0.63392	0.012
27DAP/reference	0.71864	0.014
39DAP/reference	1.22079	0.603
41DAP/reference	1.00038	0.814
42DAP/reference	2.20923	0.001
43DAP/reference	2.51712	0.006
47DAP/reference	1.91309	0.001
52DAP/reference	1.08661	0.453
57DAP/reference	1.56351	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22449	0.127
27DAP/17DAP	0.90292	0.724
39DAP/27DAP	9.32995	0.016
41DAP/39DAP	0.17818	0.013
42DAP/41DAP	4.33726	0.002
43DAP/42DAP	5.61295	0.013
47DAP/43DAP	0.78807	0.104
52DAP/47DAP	0.92353	0.753
57DAP/52DAP	1.02639	0.984
57DAP/7DAP	5.39372	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.19449	0.047
17DAP/reference	0.14701	0.011
27DAP/reference	0.21766	0.01
39DAP/reference	0.55761	0.023
41DAP/reference	0.34371	0.015
42DAP/reference	1.07805	0.582
43DAP/reference	1.51469	0.02
47DAP/reference	2.37572	0.014
52DAP/reference	0.55993	0.012
57DAP/reference	0.57056	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47869	0.011
17DAP/reference	0.44547	0.003
27DAP/reference	0.4915	0.006
39DAP/reference	0.48467	0.008
41DAP/reference	0.53424	0.014
42DAP/reference	0.69113	0.021
43DAP/reference	0.42898	0.002
47DAP/reference	0.78615	0.016
52DAP/reference	0.49381	0.003
57DAP/reference	0.49915	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.19066	0.028
17DAP/reference	0.84851	0.143
27DAP/reference	0.23285	0.025
39DAP/reference	0.33772	0.007
41DAP/reference	0.47015	0.018
42DAP/reference	3.59515	0.006
43DAP/reference	3.5036	0.006
47DAP/reference	2.6468	0.005
52DAP/reference	2.8365	0.028
57DAP/reference	1.09087	0.648

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99635	1
26DAP/20DAP	0.93038	1
34DAP/26DAP	1.01423	1
51DAP/34DAP	0.9325	0.722
52DAP/51DAP	0.81632	1
53DAP/52DAP	0.84213	0.715
55DAP/53DAP	1.06334	0.781
57DAP/55DAP	1.13864	1
62DAP/57DAP	1.20549	0.833
68DAP/62DAP	1.18973	0.713
68DAP/14DAP	0.87656	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	80.3416	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	0.1458	0.017
Immature Eggplant/Mature Eggplant	3.13254	0.056
Ripe Pepper/Ripe Tomato	0.05079	0.224
Mature Eggplant/Ripe Tomato	0.04425	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.19979	0.591
1-1-2/M82	1.02036	1
12-2/M82	0.98731	1
12-4/M82	1.01523	1
1-3/M82	1.33877	1
2-1-1/M82	0.90829	0.784
2-1/M82	0.97874	1
2-6/M82	1.00111	1
3-2/M82	1.0871	0.549
4-1-1/M82	1.00391	1
4-1/M82	1.47485	0.853
4-3-2/M82	0.92367	1
4-3/M82	0.95464	1
5-3/M82	1.00224	1
6-2/M82	0.97793	1
6-3/M82	1.06176	1
7-1/M82	1.04704	0.87
7-2/M82	1.00942	1
9-3-2/M82	0.80318	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.03051	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.07732	1
IL12-4/WTpooled	1.22071	0.624
IL1-4/WTpooled	0.94419
WT/WTpooled	1.0022	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	1.17008	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06591	0.774
DC3000/delta hrp 6h	1.35274
DC3000/delta hrp 12h	1.07168	1
DC3000/delta hrp 24h	0.73658	0.034

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91356	0.265
Exp 36h	0.1401	1
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	N/A	N/A
Var 0h	0.6315	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.42604	0.229
transgenic ySAMdc/azygous control (breaker)	1.02149	1
transgenic ySAMdc/azygous control (red)	0.93873	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.23463	0.04

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.49981	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.40034	0.307
Manapal/WT (break)	1.05218	0.183
Manapal/WT (red)	0.89261	0.315