Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.15.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77765	0.077
27DAP/17DAP	0.9698	0.982
39DAP/27DAP	0.88249	0.495
41DAP/39DAP	1.16593	0.58
42DAP/41DAP	1.1582	0.903
43DAP/42DAP	1.04959	1
47DAP/43DAP	1.54471	0.181
52DAP/47DAP	0.83867	0.586
57DAP/52DAP	1.25908	0.826

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9267	0.308
17DAP/reference	0.78955	0.053
27DAP/reference	0.76996	0.041
39DAP/reference	0.73578	0.02
41DAP/reference	0.63218	0.009
42DAP/reference	0.89381	0.017
43DAP/reference	0.76871	0.029
47DAP/reference	0.68954	0.001
52DAP/reference	0.63721	0.016
57DAP/reference	0.82518	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91367	0.496
27DAP/17DAP	0.96049	0.821
39DAP/27DAP	0.84209	0.173
41DAP/39DAP	1.04135	1
42DAP/41DAP	0.906	0.486
43DAP/42DAP	0.94148	0.538
47DAP/43DAP	1.01786	0.951
52DAP/47DAP	0.97799	0.917
57DAP/52DAP	1.22068	0.305
57DAP/7DAP	1.02336	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21721	0.201
17DAP/reference	1.18553	0.437
27DAP/reference	0.7614	0.013
39DAP/reference	0.93047	0.109
41DAP/reference	0.76499	0.018
42DAP/reference	0.77301	0.022
43DAP/reference	0.73701	0.018
47DAP/reference	0.78155	0.101
52DAP/reference	0.73968	0.014
57DAP/reference	0.7277	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67508	0.009
17DAP/reference	0.76267	0.036
27DAP/reference	0.91662	0.282
39DAP/reference	0.68656	0.019
41DAP/reference	0.90829	0.237
42DAP/reference	0.98257	0.534
43DAP/reference	0.69391	0.017
47DAP/reference	0.98601	0.559
52DAP/reference	0.61984	0.004
57DAP/reference	0.52251	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23374	0.045
17DAP/reference	1.43102	0.093
27DAP/reference	0.89859	0.14
39DAP/reference	0.91134	0.179
41DAP/reference	0.90448	0.264
42DAP/reference	0.93585	0.445
43DAP/reference	0.86479	0.15
47DAP/reference	0.71716	0.025
52DAP/reference	0.70642	0.086
57DAP/reference	1.34865	0.043

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00738	1
26DAP/20DAP	0.86775	0.317
34DAP/26DAP	1.07563	0.819
51DAP/34DAP	0.90289	0.532
52DAP/51DAP	1.00814	1
53DAP/52DAP	1.15932	0.623
55DAP/53DAP	1.1221	0.547
57DAP/55DAP	1.11997	0.881
62DAP/57DAP	1.0257	1
68DAP/62DAP	0.97066	0.81
68DAP/14DAP	0.79036	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73684	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.56191	0.058
Mature Green Tomato/Ripe Tomato	1.18422	0.632
Immature Eggplant/Mature Eggplant	0.56954	0.062
Ripe Pepper/Ripe Tomato	6.27238	1
Mature Eggplant/Ripe Tomato	9.96539	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.87453

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0258	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.77747
IL1-4/WTpooled	0.94695	1
WT/WTpooled	0.99631	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	0.69656	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09463	0.921
DC3000/delta hrp 6h	0.993	0.95
DC3000/delta hrp 12h	1.22255	1
DC3000/delta hrp 24h	1.08487	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85109	0.044
DC3000 delta B/DC3000 delta AB	0.87765	0.152

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97444	1
Exp 36h	0.92006	0.623
Exp 60h	0.84182	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94775	1
Var 0h	0.90274	0.782
Var 12h I row2-row1	0.70182	0.514
Var 12h NI row2-row1	1.15965	0.649
Var 36h I row2-row1	0.96856	1
Var 36h NI row2-row1	1.11402	1
Var 60h I row2-row1	1.18246	0.562
Var 60h NI row2-row1	1.02915	1
Time course 0hI-0hNI	0.99058	1
Time course 12hI-12hNI	0.94938	0.42
Time course 36hI-36hNI	0.81414	0.023
Time course 60hI-60hNI	0.30879	0.006

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)	1.04379	0.921
transgenic ySAMdc/azygous control (breaker)	2.10162	0.166
transgenic ySAMdc/azygous control (red)	0.95973	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.64841	0.101

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.85645	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	17.7895	0.083
Manapal/WT (break)	5.49403	0.123
Manapal/WT (red)	2.21599	0.413