Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.4.4.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86212	0.511
27DAP/17DAP	1.17568	0.852
39DAP/27DAP	0.80399	0.512
41DAP/39DAP	1.18947	0.483
42DAP/41DAP	1.45408	0.223
43DAP/42DAP	1.04913	1
47DAP/43DAP	0.9587	0.815
52DAP/47DAP	1.11114	0.886
57DAP/52DAP	1.20518	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84069	0.031
17DAP/reference	0.93447	0.342
27DAP/reference	0.93551	0.417
39DAP/reference	0.87679	0.083
41DAP/reference	0.81539	0.026
42DAP/reference	0.87756	0.023
43DAP/reference	1.11291	0.34
47DAP/reference	0.98772	0.535
52DAP/reference	0.92159	0.258
57DAP/reference	1.04003	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0029	0.899
27DAP/17DAP	1.0468	0.915
39DAP/27DAP	1.02682	0.845
41DAP/39DAP	1.05304	0.79
42DAP/41DAP	1.06987	0.773
43DAP/42DAP	1.04204	0.699
47DAP/43DAP	1.30762	0.758
52DAP/47DAP	0.9482	0.807
57DAP/52DAP	1.10254	0.483
57DAP/7DAP	1.29484	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07836	0.761
17DAP/reference	1.21091	0.123
27DAP/reference	1.21491	0.06
39DAP/reference	1.15187	0.186
41DAP/reference	1.07245	0.402
42DAP/reference	1.11381	0.534
43DAP/reference	0.91721	0.241
47DAP/reference	0.9	0.293
52DAP/reference	0.89933	0.196
57DAP/reference	1.04696	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83762	0.286
17DAP/reference	0.79295	0.062
27DAP/reference	0.86574	0.22
39DAP/reference	0.92364	0.348
41DAP/reference	0.79625	0.1
42DAP/reference	0.87351	0.261
43DAP/reference	0.75834	0.032
47DAP/reference	0.80676	0.073
52DAP/reference	1.02819	1
57DAP/reference	0.79327	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09135	0.793
17DAP/reference	1.0783	1
27DAP/reference	1.07584	0.777
39DAP/reference	1.13068	0.773
41DAP/reference	1.06478	0.486
42DAP/reference	1.04268	0.994
43DAP/reference	1.12561	0.688
47DAP/reference	0.911	0.207
52DAP/reference	1.14024	0.412
57DAP/reference	1.046	0.758

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.268	0.966
26DAP/20DAP	1.01772	1
34DAP/26DAP	0.83526	0.472
51DAP/34DAP	1.36792	0.121
52DAP/51DAP	1.13383	0.704
53DAP/52DAP	0.93517	0.772
55DAP/53DAP	1.15131	0.566
57DAP/55DAP	1.00443	0.923
62DAP/57DAP	0.87788	0.681
68DAP/62DAP	1.67296	0.448
68DAP/14DAP	1.03268	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93102	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.28856	0.11
Mature Green Tomato/Ripe Tomato	1.12335	0.015
Immature Eggplant/Mature Eggplant	0.66456	0.197
Ripe Pepper/Ripe Tomato	1.36745	1
Mature Eggplant/Ripe Tomato	1.52142	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9793	N/A
1-1-2/M82	1.44927	N/A
12-2/M82	N/A	N/A
12-4/M82	0.97376	0.619
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	1.39787	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	1.04568	N/A
7-1/M82	N/A	N/A
7-2/M82	0.91388	N/A
9-3-2/M82	1.12734	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11549	0.659
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9734	1
IL12-4/WTpooled	0.94277	1
IL1-4/WTpooled	1.0148	N/A
WT/WTpooled	0.96358	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	1.04249	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87415	1
DC3000/delta hrp 6h	1.09604	0.95
DC3000/delta hrp 12h	0.82372	1
DC3000/delta hrp 24h	1.29856	0.118

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71212	N/A
DC3000 delta B/DC3000 delta AB	0.98395	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.41742	1
Exp 60h	1.31835	1

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	1.36137	N/A
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)	1.02356	0.654
transgenic ySAMdc/azygous control (breaker)	1.11112	0.248
transgenic ySAMdc/azygous control (red)	1.02672	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99591	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89958	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95868	1
Manapal/WT (break)	1.11342	1
Manapal/WT (red)	0.87773	0.242