Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.4.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.87227	0.037
27DAP/17DAP	0.93115	0.791
39DAP/27DAP	0.95145	0.67
41DAP/39DAP	0.92353	0.67
42DAP/41DAP	1.1197	0.873
43DAP/42DAP	0.6026	0.454
47DAP/43DAP	0.58274	0.064
52DAP/47DAP	0.76533	0.551
57DAP/52DAP	1.02951	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75719	0.025
17DAP/reference	1.30544	0.306
27DAP/reference	1.26325	0.014
39DAP/reference	0.91886	0.261
41DAP/reference	0.96787	0.542
42DAP/reference	0.90439	0.016
43DAP/reference	0.96085	0.538
47DAP/reference	0.87388	0.015
52DAP/reference	0.82834	0.037
57DAP/reference	0.84457	0.027

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20855	0.047
27DAP/17DAP	0.84791	0.339
39DAP/27DAP	0.99689	1
41DAP/39DAP	0.92871	0.781
42DAP/41DAP	0.99621	0.872
43DAP/42DAP	0.87131	0.027
47DAP/43DAP	0.96829	0.846
52DAP/47DAP	1.0423	0.856
57DAP/52DAP	0.86877	0.213
57DAP/7DAP	1.13134	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25032	0.093
17DAP/reference	1.67423	0.006
27DAP/reference	1.58277	0.011
39DAP/reference	2.75616	0.006
41DAP/reference	2.50364	0.011
42DAP/reference	2.96617	0.006
43DAP/reference	2.50755	0.008
47DAP/reference	1.55288	0.504
52DAP/reference	1.88923	0.013
57DAP/reference	1.54424	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88654	0.329
17DAP/reference	0.71738	0.004
27DAP/reference	0.98105	0.576
39DAP/reference	1.26302	0.377
41DAP/reference	0.92027	0.218
42DAP/reference	0.86678	0.073
43DAP/reference	0.75191	0.048
47DAP/reference	0.77605	0.027
52DAP/reference	0.77215	0.005
57DAP/reference	0.74781	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39813	0.017
17DAP/reference	1.25523	0.264
27DAP/reference	1.84779	0.02
39DAP/reference	1.55021	0.014
41DAP/reference	1.50134	0.044
42DAP/reference	1.32684	0.111
43DAP/reference	1.27651	0.1
47DAP/reference	0.79167	0.009
52DAP/reference	1.1726	0.609
57DAP/reference	1.4157	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04183	1
26DAP/20DAP	0.81258	0.317
34DAP/26DAP	1.01624	1
51DAP/34DAP	0.94392	0.563
52DAP/51DAP	1.02202	0.808
53DAP/52DAP	0.88033	0.386
55DAP/53DAP	0.9847	0.838
57DAP/55DAP	1.02772	1
62DAP/57DAP	0.90946	0.871
68DAP/62DAP	1.57935	0.182
68DAP/14DAP	1.45888	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70835	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.77598	0.058
Mature Green Tomato/Ripe Tomato	13.8518	0.015
Immature Eggplant/Mature Eggplant	2.74472	0.05
Ripe Pepper/Ripe Tomato	50.0504	0.258
Mature Eggplant/Ripe Tomato	15.4837	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.00754
12-2/M82	N/A	N/A
12-4/M82	0.74875
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	0.74909
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	1.79247
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.71907
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	0.78882
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.84351	1
IL12-4/WTpooled	0.89739	0.71
IL1-4/WTpooled	0.88434	0.562
WT/WTpooled	1.00968	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	1.09677	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.12715	0.582
DC3000/delta hrp 12h	1.18976	1
DC3000/delta hrp 24h	0.6866	0.124

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67556	0.025
DC3000 delta B/DC3000 delta AB	0.72475	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02001	1
Exp 36h	0.78493	0.623
Exp 60h	0.94991	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.06124	0.98
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.99809	0.931
transgenic ySAMdc/azygous control (breaker)	5.50022	0.162
transgenic ySAMdc/azygous control (red)	1.57154	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.88619	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.24947	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	12.5759	0.083
Manapal/WT (break)	4.84179	0.13
Manapal/WT (red)	11.6233	0.134