Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.15.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89076	0.551
27DAP/17DAP	0.76657	0.271
39DAP/27DAP	0.95699	0.67
41DAP/39DAP	0.90592	0.65
42DAP/41DAP	0.8661	1
43DAP/42DAP	1.26611	0.553
47DAP/43DAP	0.95072	0.76
52DAP/47DAP	0.73856	0.461
57DAP/52DAP	1.07136	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02167	1
17DAP/reference	0.69861	0.007
27DAP/reference	0.67485	0.022
39DAP/reference	0.78019	0.039
41DAP/reference	0.64412	0.011
42DAP/reference	0.73819	0.002
43DAP/reference	0.74902	0.024
47DAP/reference	0.74533	0.002
52DAP/reference	0.6814	0.021
57DAP/reference	0.87961	0.112

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96114	0.613
27DAP/17DAP	0.94946	0.854
39DAP/27DAP	0.77666	0.061
41DAP/39DAP	1.00854	1
42DAP/41DAP	0.91559	0.384
43DAP/42DAP	0.80089	0.034
47DAP/43DAP	1.0202	0.956
52DAP/47DAP	1.03114	0.956
57DAP/52DAP	1.04907	0.871
57DAP/7DAP	0.44717	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84042	0.1
17DAP/reference	0.76508	0.012
27DAP/reference	0.81447	0.011
39DAP/reference	0.80566	0.011
41DAP/reference	0.73354	0.012
42DAP/reference	0.71643	0.01
43DAP/reference	0.69748	0.011
47DAP/reference	0.74121	0.057
52DAP/reference	0.58856	0.012
57DAP/reference	0.6691	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93789	0.441
17DAP/reference	0.67865	0.02
27DAP/reference	0.65542	0.008
39DAP/reference	0.55039	0.011
41DAP/reference	0.66774	0.009
42DAP/reference	0.58259	0.012
43DAP/reference	0.88361	0.236
47DAP/reference	0.64562	0.009
52DAP/reference	0.56421	0.006
57DAP/reference	0.65854	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80078	0.098
17DAP/reference	0.78387	0.121
27DAP/reference	0.70128	0.03
39DAP/reference	0.70665	0.008
41DAP/reference	0.79352	0.027
42DAP/reference	0.70321	0.02
43DAP/reference	0.6167	0.024
47DAP/reference	0.65089	0.008
52DAP/reference	0.66643	0.049
57DAP/reference	0.60719	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96529	1
26DAP/20DAP	1.05318	0.818
34DAP/26DAP	1.00058	1
51DAP/34DAP	0.87506	0.292
52DAP/51DAP	1.01375	0.965
53DAP/52DAP	0.91224	0.595
55DAP/53DAP	0.67255	0.023
57DAP/55DAP	0.96513	0.795
62DAP/57DAP	1.24594	0.622
68DAP/62DAP	1.11383	1
68DAP/14DAP	0.64903	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.39871	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.39484	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
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	1.71445
4-3/M82	0.93746
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	2.41458

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.81718	0.243
IL2-6/WTpooled	1.27917	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.73308	1
IL12-4/WTpooled	1.10743	0.557
IL1-4/WTpooled	1.03959	1
WT/WTpooled	1.01233	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	0.78564	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13182	1
DC3000/delta hrp 6h	1.71078
DC3000/delta hrp 12h	0.41649	1
DC3000/delta hrp 24h	1.30352

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62706	0.023
DC3000 delta B/DC3000 delta AB	0.59856	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75123	1
Exp 36h	0.86907	0.699
Exp 60h	0.6682	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05242	1
Var 0h	0.46486	0.204
Var 12h I row2-row1	0.76436	0.338
Var 12h NI row2-row1	0.89019	0.713
Var 36h I row2-row1	0.93313	1
Var 36h NI row2-row1	1.3043	0.482
Var 60h I row2-row1	0.93761	0.285
Var 60h NI row2-row1	1.11706	0.904
Time course 0hI-0hNI	1.07734	0.833
Time course 12hI-12hNI	1.00011	1
Time course 36hI-36hNI	0.95267	0.389
Time course 60hI-60hNI	0.16828	0.005

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)	1.19031	0.408
transgenic ySAMdc/azygous control (breaker)	1.21866	0.248
transgenic ySAMdc/azygous control (red)	1.03969	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97168	0.22

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14724	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99684	1
Manapal/WT (break)	1.09603	1
Manapal/WT (red)	N/A	N/A