Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49464	0.403
27DAP/17DAP	1.1451	1
39DAP/27DAP	0.97293	0.769
41DAP/39DAP	0.88875	0.59
42DAP/41DAP	1.77983	0.08
43DAP/42DAP	1.08995	1
47DAP/43DAP	1.24889	0.633
52DAP/47DAP	0.74227	0.378
57DAP/52DAP	1.39201	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80685	0.101
17DAP/reference	0.78754	0.074
27DAP/reference	1.04318	0.885
39DAP/reference	0.81066	0.149
41DAP/reference	0.74674	0.085
42DAP/reference	0.89803	0.046
43DAP/reference	0.93758	0.519
47DAP/reference	1.20869	0.478
52DAP/reference	1.03716	1
57DAP/reference	1.2829	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15743	0.172
27DAP/17DAP	0.93485	0.887
39DAP/27DAP	0.86149	0.156
41DAP/39DAP	0.79943	0.599
42DAP/41DAP	1.21649	0.55
43DAP/42DAP	1.47632	0.014
47DAP/43DAP	0.97973	0.909
52DAP/47DAP	1.02845	0.927
57DAP/52DAP	1.229	0.476
57DAP/7DAP	1.25653	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12155	0.589
17DAP/reference	1.27572	0.134
27DAP/reference	1.34846	0.16
39DAP/reference	1.41379	0.028
41DAP/reference	1.03534	0.949
42DAP/reference	1.32809	0.046
43DAP/reference	1.26184	0.031
47DAP/reference	1.03617	0.948
52DAP/reference	1.23968	0.081
57DAP/reference	1.18629	0.07

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88268	0.306
17DAP/reference	0.68442	0.009
27DAP/reference	0.92574	0.212
39DAP/reference	1.00168	0.682
41DAP/reference	0.97305	0.432
42DAP/reference	0.83671	0.039
43DAP/reference	0.84987	0.269
47DAP/reference	0.90393	0.154
52DAP/reference	0.85563	0.055
57DAP/reference	0.91437	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14526	0.149
17DAP/reference	1.35448	0.237
27DAP/reference	1.21691	0.035
39DAP/reference	1.19903	0.116
41DAP/reference	1.18648	0.174
42DAP/reference	1.1763	0.171
43DAP/reference	1.15396	0.375
47DAP/reference	0.77191	0.024
52DAP/reference	1.84649	0.428
57DAP/reference	1.3922	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10095	0.966
26DAP/20DAP	0.93414	1
34DAP/26DAP	0.90889	0.712
51DAP/34DAP	1.44059	0.059
52DAP/51DAP	0.83452	0.151
53DAP/52DAP	0.75175	0.069
55DAP/53DAP	0.61736	0.149
57DAP/55DAP	0.67473	0.026
62DAP/57DAP	0.99077	1
68DAP/62DAP	0.99732	0.885
68DAP/14DAP	1.4065	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7794	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6135	0.162
Mature Green Tomato/Ripe Tomato	0.62297	0.029
Immature Eggplant/Mature Eggplant	0.42663
Ripe Pepper/Ripe Tomato	2.10989	1
Mature Eggplant/Ripe Tomato	0.8109	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.41355	1
12-2/M82	N/A	N/A
12-4/M82	0.91402	1
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	1.06547
3-2/M82	1.08078
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.46209
4-3/M82	N/A	N/A
5-3/M82	0.92181	1
6-2/M82	1.94445
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	1.52631	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93359	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.16334	0.362
IL12-4/WTpooled	1.07294	0.785
IL1-4/WTpooled	1.00112
WT/WTpooled	0.95447	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	0.89297	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90157	0.839
DC3000/delta hrp 6h	0.99811	0.95
DC3000/delta hrp 12h	1.01284	1
DC3000/delta hrp 24h	0.76647	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91016	0.597
DC3000 delta B/DC3000 delta AB	0.96524

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0877	1
Exp 36h	0.84229	0.504
Exp 60h	1.05115	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02378	1
Var 0h	0.91799	0.457
Var 12h I row2-row1	0.86239	0.353
Var 12h NI row2-row1	1.04345	0.34
Var 36h I row2-row1	1.062	0.908
Var 36h NI row2-row1	1.25199	0.276
Var 60h I row2-row1	1.03113	1
Var 60h NI row2-row1	1.09098	0.904
Time course 0hI-0hNI	0.97874	0.934
Time course 12hI-12hNI	0.99413	1
Time course 36hI-36hNI	0.90457	0.125
Time course 60hI-60hNI	0.37662	0.006

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)	0.73798	0.236
transgenic ySAMdc/azygous control (breaker)	1.20257	0.248
transgenic ySAMdc/azygous control (red)	0.9917	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.80379	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.90144	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.99022	0.083
Manapal/WT (break)	1.26748	0.13
Manapal/WT (red)	1.73649	0.164