Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10972	0.947
27DAP/17DAP	1.23635	0.859
39DAP/27DAP	0.99314	0.782
41DAP/39DAP	1.0621	0.994
42DAP/41DAP	0.74928	0.397
43DAP/42DAP	1.07231	1
47DAP/43DAP	0.97152	0.876
52DAP/47DAP	1.21196	0.827
57DAP/52DAP	1.2846	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87673	0.109
17DAP/reference	0.86557	0.158
27DAP/reference	1.5225	0.01
39DAP/reference	1.27387	0.049
41DAP/reference	1.226	0.365
42DAP/reference	1.0321	1
43DAP/reference	1.15331	0.021
47DAP/reference	1.20435	0.199
52DAP/reference	1.64895	0.007
57DAP/reference	1.89508	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00389	0.871
27DAP/17DAP	0.95278	0.878
39DAP/27DAP	1.15755	0.343
41DAP/39DAP	1.26551	0.115
42DAP/41DAP	0.96951	0.743
43DAP/42DAP	1.00449	1
47DAP/43DAP	1.05959	0.837
52DAP/47DAP	1.23934	0.386
57DAP/52DAP	1.58463	0.058
57DAP/7DAP	1.62504	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53284	0.058
17DAP/reference	0.98236	0.518
27DAP/reference	1.1929	0.014
39DAP/reference	1.1399	0.198
41DAP/reference	1.03255	0.745
42DAP/reference	1.13253	0.076
43DAP/reference	1.10086	0.118
47DAP/reference	1.0914	0.421
52DAP/reference	1.1304	0.247
57DAP/reference	1.16556	0.1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84431	0.248
17DAP/reference	0.73974	0.012
27DAP/reference	1.00054	0.663
39DAP/reference	0.97422	0.442
41DAP/reference	1.10757	0.372
42DAP/reference	1.18889	0.19
43DAP/reference	0.73513	0.075
47DAP/reference	0.95187	0.359
52DAP/reference	0.85975	0.005
57DAP/reference	0.70221	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29487	0.017
17DAP/reference	1.00762	0.792
27DAP/reference	1.20397	0.085
39DAP/reference	1.07988	0.342
41DAP/reference	1.00671	0.984
42DAP/reference	1.20338	0.327
43DAP/reference	1.11885	0.625
47DAP/reference	1.04868	1
52DAP/reference	1.07999	0.694
57DAP/reference	2.2256	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28236	0.966
26DAP/20DAP	1.06821	0.683
34DAP/26DAP	1.10636	1
51DAP/34DAP	1.32836	0.1
52DAP/51DAP	0.73706	0.151
53DAP/52DAP	1.12041	0.47
55DAP/53DAP	0.84651	0.293
57DAP/55DAP	0.7716	0.246
62DAP/57DAP	1.19564	0.393
68DAP/62DAP	2.25636	0.21
68DAP/14DAP	2.03637	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.37437	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.14313	0.089
Mature Green Tomato/Ripe Tomato	0.99583	0.66
Immature Eggplant/Mature Eggplant	0.91588	0.366
Ripe Pepper/Ripe Tomato	0.76193	0.224
Mature Eggplant/Ripe Tomato	0.91051	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.53763	0.536
1-1-2/M82	0.99106	1
12-2/M82	0.94089	0.955
12-4/M82	0.75388	0.619
1-3/M82	1.42461	0.479
2-1-1/M82	0.83667	0.92
2-1/M82	0.70026
2-6/M82	0.64683	1
3-2/M82	N/A	N/A
4-1-1/M82	0.54619
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.75245	0.578
5-3/M82	1.03238	1
6-2/M82	0.83538	1
6-3/M82	0.95868	1
7-1/M82	0.96266	1
7-2/M82	0.9522	1
9-3-2/M82	0.76875	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.73734	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.21037	1
IL12-4/WTpooled	1.11849	0.785
IL1-4/WTpooled	0.81483
WT/WTpooled	1.07138	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	1.0259	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05923	0.921
DC3000/delta hrp 6h	0.91812	0.95
DC3000/delta hrp 12h	0.9779	1
DC3000/delta hrp 24h	1.57423	0.041

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.62194	0.29
DC3000 delta B/DC3000 delta AB	1.51781	0.193

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00473	1
Exp 36h	1.16912	0.693
Exp 60h	1.49619	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99871
Var 0h	0.6619	0.332
Var 12h I row2-row1	0.99901	1
Var 12h NI row2-row1	1.24117	0.235
Var 36h I row2-row1	0.98967	1
Var 36h NI row2-row1	0.88298	0.264
Var 60h I row2-row1	0.80996	0.374
Var 60h NI row2-row1	0.71711	0.292
Time course 0hI-0hNI	1.1553	0.603
Time course 12hI-12hNI	1.14957	0.145
Time course 36hI-36hNI	1.68654	0.006
Time course 60hI-60hNI	2.62262	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)	1.19023	0.273
transgenic ySAMdc/azygous control (breaker)	0.78567	0.251
transgenic ySAMdc/azygous control (red)	0.94125	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03628	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.48244	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8303	1
Manapal/WT (break)	0.86367	1
Manapal/WT (red)	0.9083	0.424