Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81459	0.318
27DAP/17DAP	1.22098	0.766
39DAP/27DAP	0.87081	0.549
41DAP/39DAP	1.35478	0.403
42DAP/41DAP	1.11909	0.983
43DAP/42DAP	1.11831	0.899
47DAP/43DAP	0.99899	0.84
52DAP/47DAP	1.68066	0.204
57DAP/52DAP	0.9965	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97596	0.55
17DAP/reference	1.09332	0.138
27DAP/reference	1.02559	0.88
39DAP/reference	1.15886	0.026
41DAP/reference	1.03237	0.963
42DAP/reference	0.97764	0.372
43DAP/reference	1.03868	0.838
47DAP/reference	0.99326	0.568
52DAP/reference	0.64407	0.018
57DAP/reference	0.77908	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07634	0.975
27DAP/17DAP	1.09695	0.735
39DAP/27DAP	1.15984	0.388
41DAP/39DAP	1.0452	1
42DAP/41DAP	1.04771	0.976
43DAP/42DAP	1.21569	0.086
47DAP/43DAP	1.01835	0.901
52DAP/47DAP	1.09276	0.779
57DAP/52DAP	1.45374	0.357
57DAP/7DAP	1.32605	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80992	0.062
17DAP/reference	0.94838	0.167
27DAP/reference	1.01488	0.974
39DAP/reference	0.90818	0.034
41DAP/reference	0.82068	0.023
42DAP/reference	0.78821	0.01
43DAP/reference	0.83306	0.014
47DAP/reference	0.85286	0.079
52DAP/reference	0.76838	0.02
57DAP/reference	0.84678	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07989	0.507
17DAP/reference	1.0686	0.229
27DAP/reference	0.8039	0.058
39DAP/reference	0.88364	0.147
41DAP/reference	0.89987	0.13
42DAP/reference	0.82303	0.018
43DAP/reference	1.07326	0.462
47DAP/reference	0.97846	0.473
52DAP/reference	0.99013	0.576
57DAP/reference	1.44733	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88434	0.098
17DAP/reference	0.99429	0.81
27DAP/reference	1.07781	0.188
39DAP/reference	1.1213	0.081
41DAP/reference	1.01938	0.889
42DAP/reference	0.93109	0.445
43DAP/reference	0.90082	0.416
47DAP/reference	1.03865	1
52DAP/reference	1.3445	0.241
57DAP/reference	0.59325	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89821	0.961
26DAP/20DAP	0.99199	1
34DAP/26DAP	0.93602	0.848
51DAP/34DAP	0.95842	0.737
52DAP/51DAP	1.00432	1
53DAP/52DAP	1.05253	0.935
55DAP/53DAP	1.08725	0.764
57DAP/55DAP	0.87059	0.532
62DAP/57DAP	1.24414	0.723
68DAP/62DAP	1.10623	0.864
68DAP/14DAP	0.70689	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9426	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.54926	0.019
Immature Eggplant/Mature Eggplant	0.90864	0.912
Ripe Pepper/Ripe Tomato	0.61534	0.224
Mature Eggplant/Ripe Tomato	0.92832

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01661	1
1-1-2/M82	0.87754	0.804
12-2/M82	1.2523	1
12-4/M82	1.21598
1-3/M82	0.89459	1
2-1-1/M82	1.1018	1
2-1/M82	N/A	N/A
2-6/M82	0.94006
3-2/M82	N/A	N/A
4-1-1/M82	1.15133	0.874
4-1/M82	0.51573
4-3-2/M82	0.94371	1
4-3/M82	0.9069	1
5-3/M82	0.91717	1
6-2/M82	0.8567	1
6-3/M82	N/A	N/A
7-1/M82	1.14569	0.925
7-2/M82	0.77133
9-3-2/M82	1.08843	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93355	0.247
IL2-6/WTpooled	0.73475	0.473
IL7-5/WTpooled	0.53011	1
IL7-3/WTpooled	1.60036	0.362
IL12-4/WTpooled	1.0866	0.785
IL1-4/WTpooled	1.15191	1
WT/WTpooled	1.04184	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	1.17659	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.36195	0.921
DC3000/delta hrp 6h	1.21673	1
DC3000/delta hrp 12h	0.92373	1
DC3000/delta hrp 24h	1.03639	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99951	1
DC3000 delta B/DC3000 delta AB	0.94287	0.511

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15623	1
Exp 36h	1.67169	0.693
Exp 60h	1.43386	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.10317	1
Var 0h	1.22247	0.782
Var 12h I row2-row1	1.12619	0.204
Var 12h NI row2-row1	0.89227	0.546
Var 36h I row2-row1	0.97312	1
Var 36h NI row2-row1	0.93681	0.549
Var 60h I row2-row1	1.35413	0.562
Var 60h NI row2-row1	1.12957	0.904
Time course 0hI-0hNI	1.00635	1
Time course 12hI-12hNI	1.2962	0.018
Time course 36hI-36hNI	1.25744	0.005
Time course 60hI-60hNI	0.92553	0.319

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)	0.93606	0.662
transgenic ySAMdc/azygous control (breaker)	0.99488	1
transgenic ySAMdc/azygous control (red)	1.15461	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01202	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.37163	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11754	1
Manapal/WT (break)	0.83865	1
Manapal/WT (red)	0.74924	0.187