Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99182	0.823
27DAP/17DAP	0.97735	1
39DAP/27DAP	1.09187	1
41DAP/39DAP	1.10476	0.765
42DAP/41DAP	0.94414	1
43DAP/42DAP	0.98642	0.93
47DAP/43DAP	1.07837	0.733
52DAP/47DAP	1.16073	0.806
57DAP/52DAP	1.27156	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78559	0.067
17DAP/reference	0.88551	0.079
27DAP/reference	1.00452	0.904
39DAP/reference	0.81194	0.031
41DAP/reference	0.77782	0.012
42DAP/reference	0.93841	0.099
43DAP/reference	0.99286	0.82
47DAP/reference	0.94934	0.207
52DAP/reference	1.07665	0.272
57DAP/reference	1.01748	0.805

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04069	1
27DAP/17DAP	1.08079	0.761
39DAP/27DAP	0.9669	0.768
41DAP/39DAP	0.99022	1
42DAP/41DAP	0.86749	0.332
43DAP/42DAP	1.16926	0.25
47DAP/43DAP	0.97129	0.861
52DAP/47DAP	1.09063	0.756
57DAP/52DAP	0.85901	0.322
57DAP/7DAP	0.93226	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33561	0.106
17DAP/reference	0.99054	0.518
27DAP/reference	1.25151	0.551
39DAP/reference	1.07895	0.909
41DAP/reference	1.19562	0.153
42DAP/reference	1.07282	0.889
43DAP/reference	1.03245	1
47DAP/reference	1.1057	0.386
52DAP/reference	1.315	0.028
57DAP/reference	1.1126	0.382

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86897	0.119
17DAP/reference	0.7046	0.004
27DAP/reference	0.87885	0.155
39DAP/reference	0.91512	0.076
41DAP/reference	0.92041	0.284
42DAP/reference	0.86244	0.039
43DAP/reference	0.6037	0.004
47DAP/reference	0.81968	0.012
52DAP/reference	0.91628	0.047
57DAP/reference	0.79142	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10353	0.676
17DAP/reference	0.93453	0.579
27DAP/reference	0.95288
39DAP/reference	0.86708	0.083
41DAP/reference	1.35776	0.072
42DAP/reference	1.00741	1
43DAP/reference	0.89664	0.267
47DAP/reference	0.90181	0.054
52DAP/reference	1.06047	0.862
57DAP/reference	1.03095	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14867	0.916
26DAP/20DAP	0.89643	0.512
34DAP/26DAP	1.18228	0.304
51DAP/34DAP	1.25482	0.143
52DAP/51DAP	1.00927	0.954
53DAP/52DAP	1.08311	0.608
55DAP/53DAP	1.01556	1
57DAP/55DAP	1.05645	0.997
62DAP/57DAP	0.9011	0.681
68DAP/62DAP	1.38426	0.178
68DAP/14DAP	2.45831	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.58149	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.86766	0.356
Mature Green Tomato/Ripe Tomato	0.97466	0.66
Immature Eggplant/Mature Eggplant	1.76448	0.085
Ripe Pepper/Ripe Tomato	1.48024	1
Mature Eggplant/Ripe Tomato	1.07215	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03018
1-1-2/M82	1.12371
12-2/M82	N/A	N/A
12-4/M82	0.7283	1
1-3/M82	0.93895
2-1-1/M82	0.90119
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	0.85589
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.21498	1
5-3/M82	1.03023	0.467
6-2/M82	1.53912	0.219
6-3/M82	1.36673
7-1/M82	N/A	N/A
7-2/M82	1.2684	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.31866	0.277
IL2-6/WTpooled	0.8805	0.348
IL7-5/WTpooled	0.94424	1
IL7-3/WTpooled	1.05004	1
IL12-4/WTpooled	1.02871	1
IL1-4/WTpooled	1.06689	1
WT/WTpooled	1.0131	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	0.88828	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06894	0.921
DC3000/delta hrp 6h	0.97787	0.95
DC3000/delta hrp 12h	1.11849	1
DC3000/delta hrp 24h	1.08238	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.5319
DC3000 delta B/DC3000 delta AB	0.89303	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99611	1
Exp 36h	1.21983	0.693
Exp 60h	1.11152	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93913	1
Var 0h	1.23488	0.98
Var 12h I row2-row1	0.99979	1
Var 12h NI row2-row1	0.99802	1
Var 36h I row2-row1	0.88551	0.805
Var 36h NI row2-row1	0.69901	0.253
Var 60h I row2-row1	1.18287
Var 60h NI row2-row1	0.99425	1
Time course 0hI-0hNI	0.95367	0.702
Time course 12hI-12hNI	1.04824	0.788
Time course 36hI-36hNI	0.78564	0.064
Time course 60hI-60hNI	0.59592	0.015

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)	0.89444	0.315
transgenic ySAMdc/azygous control (breaker)	0.79357	0.132
transgenic ySAMdc/azygous control (red)	0.99325	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05333	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05043	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16486	0.096
Manapal/WT (break)	0.92471	1
Manapal/WT (red)	0.83367	0.315