Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.18.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90142	0.464
27DAP/17DAP	0.93319	0.876
39DAP/27DAP	1.27676	0.677
41DAP/39DAP	0.94276	0.769
42DAP/41DAP	0.83092	0.774
43DAP/42DAP	1.03882	1
47DAP/43DAP	1.0865	0.555
52DAP/47DAP	0.94376	0.837
57DAP/52DAP	0.97345	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99304	0.693
17DAP/reference	0.8591	0.104
27DAP/reference	0.96814	0.525
39DAP/reference	0.91013	0.17
41DAP/reference	0.8943	0.021
42DAP/reference	1.112	0.021
43DAP/reference	1.06391	0.73
47DAP/reference	0.9643	0.322
52DAP/reference	0.99582	0.618
57DAP/reference	1.03832	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7564	0.164
27DAP/17DAP	0.97214	0.782
39DAP/27DAP	1.13881	0.77
41DAP/39DAP	1.71392	0.603
42DAP/41DAP	0.88544	0.402
43DAP/42DAP	1.84875	0.112
47DAP/43DAP	0.81135	0.305
52DAP/47DAP	0.89359	0.702
57DAP/52DAP	2.04321	0.112
57DAP/7DAP	1.48468	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40412	0.121
17DAP/reference	1.40857	0.014
27DAP/reference	1.58958	0.007
39DAP/reference	1.65591	0.006
41DAP/reference	1.5315	0.048
42DAP/reference	1.8354	0.007
43DAP/reference	1.75792	0.007
47DAP/reference	1.26785	0.124
52DAP/reference	1.34927	0.031
57DAP/reference	1.53457	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93595	0.518
17DAP/reference	1.01998	0.83
27DAP/reference	0.99206	0.686
39DAP/reference	1.19294	0.17
41DAP/reference	1.0193	1
42DAP/reference	1.19268	0.14
43DAP/reference	0.74222	0.036
47DAP/reference	1.00929	0.79
52DAP/reference	0.90868	0.143
57DAP/reference	0.86348	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.214	0.036
17DAP/reference	1.13669	0.482
27DAP/reference	1.74437	0.018
39DAP/reference	1.57052	0.01
41DAP/reference	1.24159	0.145
42DAP/reference	1.22123	0.251
43DAP/reference	1.15444	0.369
47DAP/reference	0.97431	0.452
52DAP/reference	1.62471	0.075
57DAP/reference	1.05336	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14713	0.966
26DAP/20DAP	1.36807	0.433
34DAP/26DAP	0.82201	0.148
51DAP/34DAP	1.1982	0.869
52DAP/51DAP	1.49091	0.742
53DAP/52DAP	1.44873	0.643
55DAP/53DAP	1.01069	0.904
57DAP/55DAP	0.90425	0.619
62DAP/57DAP	1.05285	1
68DAP/62DAP	1.22781	0.367
68DAP/14DAP	1.19876	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01048	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71081	0.194
Mature Green Tomato/Ripe Tomato	0.59269	0.03
Immature Eggplant/Mature Eggplant	1.02475	0.528
Ripe Pepper/Ripe Tomato	1.21248	1
Mature Eggplant/Ripe Tomato	0.89555	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.98785	1
12-2/M82	1.25637
12-4/M82	0.65657	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.7667
2-1/M82	N/A	N/A
2-6/M82	1.00471
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	2.60909
4-3/M82	1.40005	0.268
5-3/M82	0.74021	0.447
6-2/M82	0.98407
6-3/M82	0.48252
7-1/M82	0.48876
7-2/M82	1.43673
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.64842
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05481	0.921
DC3000/delta hrp 6h	1.15819	1
DC3000/delta hrp 12h	0.93432	1
DC3000/delta hrp 24h	1.0711	0.567

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	1.05564	1
Exp 36h	0.71985	0.449
Exp 60h	1.02747	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.58659
Var 0h	0.68713	0.782
Var 12h I row2-row1	1.24858	0.58
Var 12h NI row2-row1	1.36684
Var 36h I row2-row1	0.64137
Var 36h NI row2-row1	1.59475
Var 60h I row2-row1	0.90632	0.285
Var 60h NI row2-row1	0.778	1
Time course 0hI-0hNI	1.0129	1
Time course 12hI-12hNI	1.0426	1
Time course 36hI-36hNI	0.8797	0.58
Time course 60hI-60hNI	0.99707	1

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)	0.91276	0.267
transgenic ySAMdc/azygous control (breaker)	1.23541	0.248
transgenic ySAMdc/azygous control (red)	1.00594	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93958	0.057

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92377	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14339	1
Manapal/WT (break)	0.94941	1
Manapal/WT (red)	1.04371	1