Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.10.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78763	0.159
27DAP/17DAP	1.19013	0.844
39DAP/27DAP	1.33396	0.35
41DAP/39DAP	1.12409	0.88
42DAP/41DAP	1.0117	1
43DAP/42DAP	1.33178	0.772
47DAP/43DAP	0.36139	0.049
52DAP/47DAP	1.12523	0.926
57DAP/52DAP	1.01503	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09265	0.46
17DAP/reference	1.20704	0.013
27DAP/reference	0.95058	0.369
39DAP/reference	1.21615	0.119
41DAP/reference	1.05164	0.714
42DAP/reference	0.89591	0.081
43DAP/reference	0.98779	0.785
47DAP/reference	0.86511	0.019
52DAP/reference	0.78501	0.118
57DAP/reference	0.72252	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79095	0.201
27DAP/17DAP	1.94774	0.023
39DAP/27DAP	1.05915	0.799
41DAP/39DAP	0.91832	0.713
42DAP/41DAP	0.95691	0.674
43DAP/42DAP	0.9975	1
47DAP/43DAP	1.02308	0.939
52DAP/47DAP	1.13204	0.749
57DAP/52DAP	1.34464	0.171
57DAP/7DAP	0.9204	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97007	0.495
17DAP/reference	0.943	0.295
27DAP/reference	0.95378	0.264
39DAP/reference	0.97261	0.552
41DAP/reference	1.00746	0.589
42DAP/reference	1.04358	0.889
43DAP/reference	1.18145	0.118
47DAP/reference	1.46529	0.145
52DAP/reference	1.05455	0.732
57DAP/reference	1.12992	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14704	0.19
17DAP/reference	1.03253	1
27DAP/reference	0.88905	0.229
39DAP/reference	0.80806	0.108
41DAP/reference	0.78039	0.054
42DAP/reference	0.73477	0.032
43DAP/reference	1.10753	0.793
47DAP/reference	0.96502	0.168
52DAP/reference	0.811	0.025
57DAP/reference	1.20674	0.353

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93928	0.311
17DAP/reference	1.02062	0.918
27DAP/reference	0.9221	0.218
39DAP/reference	1.02326	0.733
41DAP/reference	0.91559	0.119
42DAP/reference	0.91391	0.361
43DAP/reference	0.79087	0.143
47DAP/reference	0.91497	0.335
52DAP/reference	1.38541	0.448
57DAP/reference	0.49877	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9611	1
26DAP/20DAP	2.33998	0.097
34DAP/26DAP	0.61213	0.076
51DAP/34DAP	1.70075	0.039
52DAP/51DAP	1.21994	0.171
53DAP/52DAP	1.2027	0.274
55DAP/53DAP	0.96316	0.82
57DAP/55DAP	1.28209	0.044
62DAP/57DAP	0.68958	0.162
68DAP/62DAP	1.24889	0.858
68DAP/14DAP	1.20194	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.62803	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.84891	0.336
Mature Green Tomato/Ripe Tomato	1.06552	0.898
Immature Eggplant/Mature Eggplant	1.33893	0.063
Ripe Pepper/Ripe Tomato	1.2962	1
Mature Eggplant/Ripe Tomato	1.56952	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92776	0.841
1-1-2/M82	1.09491	1
12-2/M82	1.06495	1
12-4/M82	1.15604	1
1-3/M82	0.82875	0.376
2-1-1/M82	1.01316	1
2-1/M82	1.08984	1
2-6/M82	1.11123	0.505
3-2/M82	0.68763	0.455
4-1-1/M82	1.02037	1
4-1/M82	0.9412
4-3-2/M82	0.98948	1
4-3/M82	1.22895	1
5-3/M82	0.98006	1
6-2/M82	1.08693	1
6-3/M82	1.00727	1
7-1/M82	0.86001	0.443
7-2/M82	1.12064	0.385
9-3-2/M82	1.11409	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	2.11124	0.427
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.49266	0.298
IL12-4/WTpooled	0.73963	0.71
IL1-4/WTpooled	1.46286
WT/WTpooled	1.00426	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	1.28115	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10392	0.914
DC3000/delta hrp 6h	0.77638	0.874
DC3000/delta hrp 12h	1.02031	1
DC3000/delta hrp 24h	2.20293	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.71592	0.042
DC3000 delta B/DC3000 delta AB	1.77128	0.08

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92972	1
Exp 36h	2.18889	0.326
Exp 60h	2.23086	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96379	1
Var 0h	0.73257	0.594
Var 12h I row2-row1	0.97596	0.948
Var 12h NI row2-row1	1.59552	0.281
Var 36h I row2-row1	0.83431	1
Var 36h NI row2-row1	0.75478	0.312
Var 60h I row2-row1	0.73305	0.285
Var 60h NI row2-row1	0.74759	0.318
Time course 0hI-0hNI	1.02011	1
Time course 12hI-12hNI	1.70187	0.007
Time course 36hI-36hNI	4.2169	0.004
Time course 60hI-60hNI	5.78072	0.008

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)	1.08511	0.331
transgenic ySAMdc/azygous control (breaker)	0.85376	0.251
transgenic ySAMdc/azygous control (red)	0.95828	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02586	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.6923	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.862	1
Manapal/WT (break)	0.78471	0.333
Manapal/WT (red)	1.0057	1