Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.19.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07883	0.932
27DAP/17DAP	1.28079	0.735
39DAP/27DAP	1.17735	0.974
41DAP/39DAP	1.25538	0.265
42DAP/41DAP	1.10847	1
43DAP/42DAP	1.09912	1
47DAP/43DAP	1.22026	0.481
52DAP/47DAP	1.13898	0.786
57DAP/52DAP	1.06112	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8287	0.078
17DAP/reference	0.76304	0.012
27DAP/reference	0.90903	0.257
39DAP/reference	0.78485	0.015
41DAP/reference	0.62669	0.008
42DAP/reference	0.88876	0.081
43DAP/reference	0.88672	0.17
47DAP/reference	0.98307	0.473
52DAP/reference	0.96367	0.427
57DAP/reference	1.29421	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57575	0.348
27DAP/17DAP	0.94267	0.878
39DAP/27DAP	0.89472	0.496
41DAP/39DAP	1.06712	0.781
42DAP/41DAP	0.8498	0.322
43DAP/42DAP	1.1413	0.413
47DAP/43DAP	0.90735	0.428
52DAP/47DAP	1.0749	0.742
57DAP/52DAP	1.05044	1
57DAP/7DAP	0.85259	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08644	0.344
17DAP/reference	1.17854	0.477
27DAP/reference	1.00112	0.8
39DAP/reference	1.39223	0.005
41DAP/reference	1.28312	0.018
42DAP/reference	1.34353	0.011
43DAP/reference	1.59464	0.013
47DAP/reference	1.38516	0.165
52DAP/reference	1.36978	0.048
57DAP/reference	1.26803	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72548	0.022
17DAP/reference	0.55263	0.003
27DAP/reference	0.77348	0.054
39DAP/reference	0.83686	0.036
41DAP/reference	0.92798	0.148
42DAP/reference	0.94887	0.355
43DAP/reference	0.63665	0.015
47DAP/reference	0.91725	0.123
52DAP/reference	0.7952	0.005
57DAP/reference	0.51802	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96464	0.489
17DAP/reference	0.91855	0.342
27DAP/reference	1.10354	0.12
39DAP/reference	1.05496	0.254
41DAP/reference	1.19409	0.02
42DAP/reference	1.15915	0.056
43DAP/reference	1.19552	0.25
47DAP/reference	0.97694	0.525
52DAP/reference	0.92085	0.464
57DAP/reference	1.28893	0.045

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09875	0.966
26DAP/20DAP	0.98045	1
34DAP/26DAP	1.27134	1
51DAP/34DAP	1.12241	0.597
52DAP/51DAP	0.8222	1
53DAP/52DAP	0.92631	0.848
55DAP/53DAP	0.7626	0.21
57DAP/55DAP	0.65599	0.36
62DAP/57DAP	1.53504	0.622
68DAP/62DAP	2.85925	0.014
68DAP/14DAP	1.80406	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73969	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11724	0.666
Mature Green Tomato/Ripe Tomato	0.96441	0.66
Immature Eggplant/Mature Eggplant	0.59203	0.063
Ripe Pepper/Ripe Tomato	1.62991	1
Mature Eggplant/Ripe Tomato	1.91606	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13966	1
1-1-2/M82	1.02729	1
12-2/M82	N/A	N/A
12-4/M82	0.82626	1
1-3/M82	0.48364
2-1-1/M82	1.11488
2-1/M82	N/A	N/A
2-6/M82	1.15418	0.695
3-2/M82	1.26959
4-1-1/M82	0.85342	1
4-1/M82	1.39198
4-3-2/M82	0.84331
4-3/M82	0.97611	1
5-3/M82	1.03544	1
6-2/M82	0.724
6-3/M82	1.05691	1
7-1/M82	0.90835	1
7-2/M82	1.19892	1
9-3-2/M82	0.99687

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.55973	0.243
IL2-6/WTpooled	1.32178	0.531
IL7-5/WTpooled	1.11301	0.792
IL7-3/WTpooled	0.61929	0.298
IL12-4/WTpooled	0.87436	0.71
IL1-4/WTpooled	0.90543	0.562
WT/WTpooled	0.90446	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	0.93368	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15461	0.921
DC3000/delta hrp 6h	1.12563	0.95
DC3000/delta hrp 12h	1.03918	1
DC3000/delta hrp 24h	0.96254	0.851

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.52276
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	1.00558	1
Exp 36h	1.03485	1
Exp 60h	0.86868	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99192	1
Var 0h	0.82199	0.933
Var 12h I row2-row1	0.77026	0.418
Var 12h NI row2-row1	1.32439	1
Var 36h I row2-row1	0.93489	1
Var 36h NI row2-row1	1.35437	0.482
Var 60h I row2-row1	1.20381	1
Var 60h NI row2-row1	1.37698	0.904
Time course 0hI-0hNI	0.91562	0.339
Time course 12hI-12hNI	0.97425	0.858
Time course 36hI-36hNI	0.76555	0.023
Time course 60hI-60hNI	0.26355	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)	1.15886	0.268
transgenic ySAMdc/azygous control (breaker)	0.70315	0.129
transgenic ySAMdc/azygous control (red)	1.02429	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93947	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96561	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32808	0.096
Manapal/WT (break)	1.48688	0.13
Manapal/WT (red)	1.09033	0.413