Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03999	0.951
27DAP/17DAP	0.92436	0.939
39DAP/27DAP	0.59443	0.346
41DAP/39DAP	1.0225	0.946
42DAP/41DAP	1.11748	0.894
43DAP/42DAP	1.16656	0.867
47DAP/43DAP	1.05108	0.966
52DAP/47DAP	0.87932	0.623
57DAP/52DAP	1.30108	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03544	1
17DAP/reference	1.32608	0.036
27DAP/reference	1.21454	0.082
39DAP/reference	1.45716	0.04
41DAP/reference	1.73189	0.012
42DAP/reference	1.28247	0.004
43DAP/reference	1.08362	0.812
47DAP/reference	1.29294	0.175
52DAP/reference	1.31222	0.149
57DAP/reference	0.97514	0.479

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02061	0.871
27DAP/17DAP	1.01853	1
39DAP/27DAP	1.20909	0.214
41DAP/39DAP	0.88189	0.696
42DAP/41DAP	1.13617	0.514
43DAP/42DAP	0.94694	0.558
47DAP/43DAP	1.17473	0.837
52DAP/47DAP	0.96158	0.876
57DAP/52DAP	1.02445	0.984
57DAP/7DAP	0.85824	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91788	0.246
17DAP/reference	1.03124	1
27DAP/reference	1.21884	0.026
39DAP/reference	0.93805	0.23
41DAP/reference	0.8761	0.09
42DAP/reference	0.79063	0.012
43DAP/reference	0.81971	0.066
47DAP/reference	0.90586	0.168
52DAP/reference	0.80108	0.072
57DAP/reference	0.95895	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21266	0.19
17DAP/reference	1.4471	0.229
27DAP/reference	1.64826	0.087
39DAP/reference	1.34524	0.013
41DAP/reference	1.16988	0.146
42DAP/reference	1.46356	0.011
43DAP/reference	1.57256	0.011
47DAP/reference	1.56546	0.008
52DAP/reference	1.61932	0.079
57DAP/reference	1.01154	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87124	0.169
17DAP/reference	1.09746	0.602
27DAP/reference	1.00282	0.883
39DAP/reference	1.04327	0.792
41DAP/reference	1.06779	0.205
42DAP/reference	1.1306	0.327
43DAP/reference	1.1304	0.452
47DAP/reference	1.40389	0.014
52DAP/reference	1.12325	0.509
57DAP/reference	1.44266	0.063

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17419
26DAP/20DAP	1.26249	0.464
34DAP/26DAP	0.97461	0.961
51DAP/34DAP	1.24099	0.524
52DAP/51DAP	1.10288	0.218
53DAP/52DAP	1.04207	1
55DAP/53DAP	0.77406	0.203
57DAP/55DAP	1.29269	0.854
62DAP/57DAP	0.73896	0.088
68DAP/62DAP	1.13681	0.85
68DAP/14DAP	0.97881	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06091	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.32775	0.079
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.64246	1
Mature Eggplant/Ripe Tomato	0.62055	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.01043	1
12-2/M82	N/A	N/A
12-4/M82	0.91206
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.11549	0.426
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.34329
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86653	0.321
IL2-6/WTpooled	1.08152	0.419
IL7-5/WTpooled	0.80781	1
IL7-3/WTpooled	1.09615	1
IL12-4/WTpooled	1.08297	0.785
IL1-4/WTpooled	1.0181	1
WT/WTpooled	1.0236	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	0.95242	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.001	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.11683	1
DC3000/delta hrp 24h	0.89753	0.513

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	2.38192

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05791	1
Exp 36h	0.77892	0.749
Exp 60h	1.03195	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00499
Var 0h	1.34504	0.936
Var 12h I row2-row1	1.30163	0.324
Var 12h NI row2-row1	1.07324	1
Var 36h I row2-row1	1.18198	1
Var 36h NI row2-row1	0.80983	0.706
Var 60h I row2-row1	1.08139	0.523
Var 60h NI row2-row1	0.8049	0.904
Time course 0hI-0hNI	1.03328	0.867
Time course 12hI-12hNI	1.00907	0.885
Time course 36hI-36hNI	0.95812	0.306
Time course 60hI-60hNI	0.78567	0.015

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)	0.95626	0.409
transgenic ySAMdc/azygous control (breaker)	0.89829	0.49
transgenic ySAMdc/azygous control (red)	0.87245	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0542	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01806	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.04579	1
Manapal/WT (break)	0.90775	0.333
Manapal/WT (red)	1.22697	0.413