Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.4.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24289	0.348
27DAP/17DAP	1.06055	1
39DAP/27DAP	0.74521	0.435
41DAP/39DAP	1.43634	0.398
42DAP/41DAP	1.14764	0.843
43DAP/42DAP	0.87892	0.776
47DAP/43DAP	1.35254	0.355
52DAP/47DAP	0.9982	0.908
57DAP/52DAP	1.32056	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86682	0.118
17DAP/reference	0.95389	0.474
27DAP/reference	0.93428	0.395
39DAP/reference	0.95905	0.475
41DAP/reference	0.88227	0.154
42DAP/reference	0.9539	0.124
43DAP/reference	0.98036	0.708
47DAP/reference	1.23478	0.207
52DAP/reference	1.19913	0.021
57DAP/reference	1.26237	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0096	0.871
27DAP/17DAP	0.96556	0.887
39DAP/27DAP	1.21496	0.383
41DAP/39DAP	1.01887	1
42DAP/41DAP	1.24044	0.186
43DAP/42DAP	0.96358	0.729
47DAP/43DAP	1.02251	0.969
52DAP/47DAP	1.00829	0.982
57DAP/52DAP	1.30121	0.32
57DAP/7DAP	1.47051	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00869	1
17DAP/reference	0.94695	0.22
27DAP/reference	1.19341	0.073
39DAP/reference	1.22251	0.101
41DAP/reference	1.14942	0.171
42DAP/reference	1.11046	0.308
43DAP/reference	0.9527	0.385
47DAP/reference	0.96617	0.504
52DAP/reference	1.10187	0.526
57DAP/reference	1.09069	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82836	0.306
17DAP/reference	0.85376	0.113
27DAP/reference	0.98678	0.598
39DAP/reference	1.11582	0.556
41DAP/reference	0.97132	0.493
42DAP/reference	0.8698	0.061
43DAP/reference	0.98995	0.692
47DAP/reference	1.11339	0.256
52DAP/reference	0.88588	0.22
57DAP/reference	0.91705	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1085	0.575
17DAP/reference	0.94334	0.47
27DAP/reference	0.96233	0.49
39DAP/reference	1.08307	0.365
41DAP/reference	1.09549	0.605
42DAP/reference	1.10752	0.54
43DAP/reference	1.21116	0.241
47DAP/reference	0.91811	0.296
52DAP/reference	1.02993	0.99
57DAP/reference	1.29054	0.034

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95427	1
26DAP/20DAP	1.15884	0.834
34DAP/26DAP	1.62319	0.819
51DAP/34DAP	1.20838	0.429
52DAP/51DAP	1.16491	0.446
53DAP/52DAP	1.22985	0.458
55DAP/53DAP	0.90239	0.632
57DAP/55DAP	0.97521	0.855
62DAP/57DAP	0.76571	0.162
68DAP/62DAP	0.73425	0.406
68DAP/14DAP	0.99297	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.23686	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67955	0.193
Mature Green Tomato/Ripe Tomato	0.85657	0.086
Immature Eggplant/Mature Eggplant	0.86639	0.493
Ripe Pepper/Ripe Tomato	2.07923	1
Mature Eggplant/Ripe Tomato	0.81991	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.03895
12-2/M82	0.75159
12-4/M82	0.96185	1
1-3/M82	0.70959
2-1-1/M82	0.67203	0.465
2-1/M82	N/A	N/A
2-6/M82	0.77735	1
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	1.07009
4-3/M82	0.99041	1
5-3/M82	0.87678	0.49
6-2/M82	N/A	N/A
6-3/M82	1.15164	1
7-1/M82	0.86759
7-2/M82	N/A	N/A
9-3-2/M82	0.96959

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99551	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87511	0.31
IL12-4/WTpooled	0.89243	0.71
IL1-4/WTpooled	1.18618
WT/WTpooled	0.9625	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	0.99428	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97121	1
DC3000/delta hrp 6h	0.95467	0.95
DC3000/delta hrp 12h	0.98186	1
DC3000/delta hrp 24h	1.07999	0.502

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97102	1
Exp 36h	0.85429	0.879
Exp 60h	1.10049	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	N/A	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)	0.90614	0.286
transgenic ySAMdc/azygous control (breaker)	1.0203	1
transgenic ySAMdc/azygous control (red)	0.97281	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99111	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72998	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01133	1
Manapal/WT (break)	1.03968	1
Manapal/WT (red)	1.29937	0.413