Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.7.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81288	0.098
27DAP/17DAP	1.23254	0.832
39DAP/27DAP	1.74685	0.057
41DAP/39DAP	0.67342	0.064
42DAP/41DAP	1.63847	0.679
43DAP/42DAP	1.10408	1
47DAP/43DAP	1.04973	0.926
52DAP/47DAP	0.82703	0.551
57DAP/52DAP	1.15531	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05877	0.76
17DAP/reference	0.90436	0.18
27DAP/reference	0.99175	0.741
39DAP/reference	0.89237	0.054
41DAP/reference	0.78189	0.039
42DAP/reference	0.92063	0.111
43DAP/reference	1.01526	1
47DAP/reference	0.94099	0.224
52DAP/reference	0.96721	0.416
57DAP/reference	1.14241	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93913	0.542
27DAP/17DAP	0.96146	0.748
39DAP/27DAP	1.05559	0.659
41DAP/39DAP	0.85488	0.384
42DAP/41DAP	0.94047	0.583
43DAP/42DAP	1.14675	0.061
47DAP/43DAP	0.98768	0.939
52DAP/47DAP	1.03426	0.892
57DAP/52DAP	0.87282	0.128
57DAP/7DAP	0.91269	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55238	0.041
17DAP/reference	1.19507	0.199
27DAP/reference	1.13181	0.107
39DAP/reference	1.10186	0.297
41DAP/reference	0.98053	0.538
42DAP/reference	1.24178	0.014
43DAP/reference	1.41359	0.008
47DAP/reference	1.22745	0.062
52DAP/reference	1.10793	0.071
57DAP/reference	1.00076	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09296	0.62
17DAP/reference	0.92053	0.208
27DAP/reference	1.07434	0.81
39DAP/reference	0.92538	0.178
41DAP/reference	1.10172	0.199
42DAP/reference	0.9764	0.534
43DAP/reference	0.81244	0.056
47DAP/reference	0.91932	0.083
52DAP/reference	0.92868	0.066
57DAP/reference	0.7749	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30816	0.116
17DAP/reference	0.90135	0.141
27DAP/reference	1.05027	0.621
39DAP/reference	0.97368	0.504
41DAP/reference	0.96339	0.56
42DAP/reference	1.09313	0.576
43DAP/reference	1.10251	0.744
47DAP/reference	0.96941	0.465
52DAP/reference	1.21141	0.19
57DAP/reference	1.06534	0.827

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92673	0.981
26DAP/20DAP	1.12722	0.574
34DAP/26DAP	0.92278	0.627
51DAP/34DAP	1.24426	0.047
52DAP/51DAP	0.93355	1
53DAP/52DAP	1.1558	0.678
55DAP/53DAP	1.0067	1
57DAP/55DAP	1.02153	0.961
62DAP/57DAP	1.10476	0.515
68DAP/62DAP	1.37001	0.11
68DAP/14DAP	0.80907	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.87238	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72099	0.148
Immature Eggplant/Mature Eggplant	0.43133	0.062
Ripe Pepper/Ripe Tomato	0.45315	1
Mature Eggplant/Ripe Tomato	2.12297	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82121
12-2/M82	N/A	N/A
12-4/M82	1.60035	1
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	0.90019
3-2/M82	1.24072	0.463
4-1-1/M82	N/A	N/A
4-1/M82	3.05664	0.328
4-3-2/M82	1.29883	1
4-3/M82	N/A	N/A
5-3/M82	0.70775
6-2/M82	1.22644
6-3/M82	N/A	N/A
7-1/M82	1.10209
7-2/M82	1.37671
9-3-2/M82	1.12589	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0018	1
IL12-4/WTpooled	1.09777	0.891
IL1-4/WTpooled	1.19683
WT/WTpooled	1.24172	0.911

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	1.99728	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03721	0.921
DC3000/delta hrp 6h	0.75469	0.95
DC3000/delta hrp 12h	0.72508	1
DC3000/delta hrp 24h	1.45433	0.067

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.80414	0.033
DC3000 delta B/DC3000 delta AB	0.66424	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9915	1
Var 0h	1.0642	1
Var 12h I row2-row1	0.8046	0.338
Var 12h NI row2-row1	1.03065	1
Var 36h I row2-row1	1.17852	0.908
Var 36h NI row2-row1	1.2881	1
Var 60h I row2-row1	1.04848	1
Var 60h NI row2-row1	1.00827	1
Time course 0hI-0hNI	0.92781	0.516
Time course 12hI-12hNI	1.01216	0.854
Time course 36hI-36hNI	0.9464	0.36
Time course 60hI-60hNI	0.36514	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)	1.24109	0.455
transgenic ySAMdc/azygous control (breaker)	0.78912	0.142
transgenic ySAMdc/azygous control (red)	1.16861	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96838	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81587	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1116	1
Manapal/WT (break)	0.83061	0.333
Manapal/WT (red)	1.23026	1