Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.16.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00501	0.77
27DAP/17DAP	1.36496	0.712
39DAP/27DAP	0.75596	0.338
41DAP/39DAP	0.89573	0.65
42DAP/41DAP	0.72941	0.774
43DAP/42DAP	0.69037	0.546
47DAP/43DAP	1.50492	0.609
52DAP/47DAP	1.19524	0.891
57DAP/52DAP	1.06035	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9119	0.262
17DAP/reference	1.04761	0.508
27DAP/reference	1.00076	0.847
39DAP/reference	1.07781	0.136
41DAP/reference	0.98622	0.814
42DAP/reference	0.90396	0.034
43DAP/reference	0.97335	0.675
47DAP/reference	0.91184	0.161
52DAP/reference	0.97813	0.515
57DAP/reference	1.07116	0.22

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02047	0.961
27DAP/17DAP	1.12521	0.61
39DAP/27DAP	1.01149	0.854
41DAP/39DAP	1.16021	0.663
42DAP/41DAP	0.97517	0.746
43DAP/42DAP	1.23758	0.103
47DAP/43DAP	1.0475	0.798
52DAP/47DAP	0.94721	0.807
57DAP/52DAP	0.97957	0.745
57DAP/7DAP	1.64334

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72109	0.069
17DAP/reference	0.80509	0.049
27DAP/reference	0.95478	0.325
39DAP/reference	0.8515	0.17
41DAP/reference	0.78898	0.107
42DAP/reference	0.73268	0.013
43DAP/reference	0.80576	0.027
47DAP/reference	0.83052	0.128
52DAP/reference	0.83565	0.077
57DAP/reference	0.79707	0.086

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80726	0.012
17DAP/reference	0.86239	0.086
27DAP/reference	0.85916	0.079
39DAP/reference	0.98	0.509
41DAP/reference	0.88948	0.118
42DAP/reference	0.90281	0.135
43DAP/reference	1.01861	0.692
47DAP/reference	0.8778	0.015
52DAP/reference	0.83871	0.025
57DAP/reference	0.76154	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7922	0.036
17DAP/reference	0.89886	0.3
27DAP/reference	0.84055	0.092
39DAP/reference	0.86347	0.133
41DAP/reference	0.97352	0.56
42DAP/reference	0.85773	0.071
43DAP/reference	0.81985	0.022
47DAP/reference	0.91733	0.199
52DAP/reference	0.86623	0.204
57DAP/reference	1.01363	0.858

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0138	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.01337	1
51DAP/34DAP	1.07987	0.993
52DAP/51DAP	1.27215	0.094
53DAP/52DAP	1.21543	0.187
55DAP/53DAP	0.99741	0.925
57DAP/55DAP	1.27897	0.287
62DAP/57DAP	1.32214	0.515
68DAP/62DAP	0.63921	0.314
68DAP/14DAP	0.86745	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.45098	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.28713	0.176
Mature Green Tomato/Ripe Tomato	0.87895
Immature Eggplant/Mature Eggplant	0.80116	0.134
Ripe Pepper/Ripe Tomato	2.0205	1
Mature Eggplant/Ripe Tomato	1.40726	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09347	0.742
1-1-2/M82	1.00099	1
12-2/M82	N/A	N/A
12-4/M82	0.77196	1
1-3/M82	0.80225
2-1-1/M82	1.17661
2-1/M82	N/A	N/A
2-6/M82	1.05168	1
3-2/M82	1.14737
4-1-1/M82	0.76503
4-1/M82	1.0508
4-3-2/M82	0.98912	1
4-3/M82	1.22373
5-3/M82	1.04529	1
6-2/M82	0.79224
6-3/M82	0.72446
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.19521

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.15125	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.17468	0.362
IL12-4/WTpooled	1.44346	0.595
IL1-4/WTpooled	0.87763
WT/WTpooled	1.03173	0.999

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	1.19091	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98857	1
DC3000/delta hrp 6h	1.27287	1
DC3000/delta hrp 12h	0.9482	1
DC3000/delta hrp 24h	1.06896	0.411

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	0.99034	1
Exp 36h	0.95456	0.879
Exp 60h	0.97808	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03332	1
Var 0h	0.98426	1
Var 12h I row2-row1	1.04794	0.654
Var 12h NI row2-row1	0.93918	0.546
Var 36h I row2-row1	1.05023	1
Var 36h NI row2-row1	0.83546	0.45
Var 60h I row2-row1	1.24408	0.562
Var 60h NI row2-row1	1.18419	0.904
Time course 0hI-0hNI	0.9331	0.623
Time course 12hI-12hNI	0.96685	0.802
Time course 36hI-36hNI	0.97387	0.418
Time course 60hI-60hNI	1.09169	0.673

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)	1.05043	0.326
transgenic ySAMdc/azygous control (breaker)	1.13315	0.248
transgenic ySAMdc/azygous control (red)	1.03851	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98244	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00845	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08896	1
Manapal/WT (break)	0.87672	0.333
Manapal/WT (red)	1.12605	1