Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.69578	0.173
27DAP/17DAP	0.89438	0.801
39DAP/27DAP	2.18687	0.139
41DAP/39DAP	1.15473	0.822
42DAP/41DAP	1.56891	0.131
43DAP/42DAP	0.87467	0.658
47DAP/43DAP	1.0245	0.965
52DAP/47DAP	1.09196	0.959
57DAP/52DAP	0.80774	0.86

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61084	0.024
17DAP/reference	0.8311	0.018
27DAP/reference	0.80793	0.016
39DAP/reference	0.79467	0.024
41DAP/reference	0.80808	0.014
42DAP/reference	0.83094	0.007
43DAP/reference	1.00129	0.942
47DAP/reference	0.79131	0.004
52DAP/reference	0.72277	0.018
57DAP/reference	0.79538	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.12343	0.036
27DAP/17DAP	0.48714	0.094
39DAP/27DAP	1.71522	0.045
41DAP/39DAP	0.97215	0.959
42DAP/41DAP	1.51911	0.015
43DAP/42DAP	0.69065	0.035
47DAP/43DAP	1.18326	0.045
52DAP/47DAP	0.7505	0.18
57DAP/52DAP	0.6893	0.25
57DAP/7DAP	1.20251	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.874	0.224
17DAP/reference	0.86523	0.072
27DAP/reference	0.82676	0.035
39DAP/reference	0.83139	0.039
41DAP/reference	0.75034	0.015
42DAP/reference	0.66186	0.014
43DAP/reference	0.73724	0.019
47DAP/reference	0.80606	0.128
52DAP/reference	1.06464	0.212
57DAP/reference	1.03143	0.748

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76132	0.058
17DAP/reference	0.62534	0.006
27DAP/reference	0.7021	0.026
39DAP/reference	0.68203	0.015
41DAP/reference	0.79054	0.05
42DAP/reference	0.79477	0.039
43DAP/reference	0.76541	0.018
47DAP/reference	0.85778	0.079
52DAP/reference	0.57693	0.006
57DAP/reference	0.86606	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86048	0.104
17DAP/reference	0.86319	0.313
27DAP/reference	0.83646	0.046
39DAP/reference	0.84926	0.092
41DAP/reference	0.90537	0.264
42DAP/reference	0.74432	0.071
43DAP/reference	0.79561	0.206
47DAP/reference	0.52793	0.006
52DAP/reference	0.64812	0.107
57DAP/reference	0.64615	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00266	1
26DAP/20DAP	1.04253	1
34DAP/26DAP	1.28442	0.542
51DAP/34DAP	7.39746	0.021
52DAP/51DAP	0.73343	0.151
53DAP/52DAP	1.46814	0.125
55DAP/53DAP	0.53641	0.018
57DAP/55DAP	0.74645	0.107
62DAP/57DAP	0.83211	0.28
68DAP/62DAP	1.48325	0.06
68DAP/14DAP	2.47162	0.024

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.06259	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.129	0.051
Mature Green Tomato/Ripe Tomato	1.09532	0.577
Immature Eggplant/Mature Eggplant	8.33877	0.05
Ripe Pepper/Ripe Tomato	30.761	0.256
Mature Eggplant/Ripe Tomato	9.371	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0277
12-2/M82	N/A	N/A
12-4/M82	0.89253	1
1-3/M82	N/A	N/A
2-1-1/M82	0.80369
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	2.14334	0.447
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.21499
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	0.71523	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.30286	1
IL12-4/WTpooled	0.99765	1
IL1-4/WTpooled	1.72141	1
WT/WTpooled	1.08015	0.855

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	1.8117	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.29577	0.692
DC3000/delta hrp 6h	1.28607	1
DC3000/delta hrp 12h	1.26391	1
DC3000/delta hrp 24h	0.77915	0.067

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.58561	0.045
DC3000 delta B/DC3000 delta AB	1.77849	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.54767	1
Exp 36h	1.17516	1
Exp 60h	1.76517	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04634	1
Var 0h	1.01147	1
Var 12h I row2-row1	1.49279	0.348
Var 12h NI row2-row1	1.55947	0.34
Var 36h I row2-row1	1.46605	0.309
Var 36h NI row2-row1	1.03429	1
Var 60h I row2-row1	0.58718	0.285
Var 60h NI row2-row1	1.00456	1
Time course 0hI-0hNI	1.11049	0.719
Time course 12hI-12hNI	0.96614	0.815
Time course 36hI-36hNI	1.22651	0.089
Time course 60hI-60hNI	5.95489	0.008

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)	1.38233	0.571
transgenic ySAMdc/azygous control (breaker)	1.02324	1
transgenic ySAMdc/azygous control (red)	1.14336	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.86108	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93364	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36447	0.105
Manapal/WT (break)	1.00677	1
Manapal/WT (red)	0.62273	0.315