Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87626	0.419
27DAP/17DAP	1.07919	0.873
39DAP/27DAP	1.18147	0.579
41DAP/39DAP	0.83556	0.356
42DAP/41DAP	1.03295	1
43DAP/42DAP	0.93207	0.867
47DAP/43DAP	1.067	0.793
52DAP/47DAP	1.06079	0.913
57DAP/52DAP	1.41679	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0062	1
17DAP/reference	1.03283	0.457
27DAP/reference	0.98566	0.623
39DAP/reference	1.01736	0.664
41DAP/reference	1.00542	0.963
42DAP/reference	0.90179	0.033
43DAP/reference	1.0225	0.73
47DAP/reference	0.91613	0.06
52DAP/reference	0.96251	0.319
57DAP/reference	0.95707	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96833	0.644
27DAP/17DAP	0.94686	0.475
39DAP/27DAP	1.07627	0.553
41DAP/39DAP	0.88842	0.713
42DAP/41DAP	0.94609	0.764
43DAP/42DAP	1.06913	0.176
47DAP/43DAP	0.93611	0.63
52DAP/47DAP	0.98767	0.919
57DAP/52DAP	0.99444	0.857
57DAP/7DAP	1.04276	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17248	0.444
17DAP/reference	1.6432	0.574
27DAP/reference	0.95267	0.375
39DAP/reference	1.00531	1
41DAP/reference	1.10329	0.207
42DAP/reference	0.88114	0.2
43DAP/reference	1.05763	0.707
47DAP/reference	0.85229	0.036
52DAP/reference	1.01247	0.679
57DAP/reference	1.05034	0.966

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98256	0.756
17DAP/reference	1.05965	0.236
27DAP/reference	1.06964	0.757
39DAP/reference	0.93329	0.152
41DAP/reference	0.96244	0.393
42DAP/reference	0.91576	0.061
43DAP/reference	0.99998	0.831
47DAP/reference	0.88529	0.035
52DAP/reference	0.97766	0.351
57DAP/reference	1.03076	0.64

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97918	0.607
17DAP/reference	0.98249	0.739
27DAP/reference	0.84186	0.442
39DAP/reference	1.01497	0.792
41DAP/reference	0.9135	0.371
42DAP/reference	0.86119	0.22
43DAP/reference	0.84722	0.102
47DAP/reference	0.92951	0.12
52DAP/reference	0.94488	0.538
57DAP/reference	0.76136	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02183	0.966
26DAP/20DAP	0.84202	0.512
34DAP/26DAP	1.01833	1
51DAP/34DAP	1.06366	0.84
52DAP/51DAP	0.977	1
53DAP/52DAP	1.02645	0.921
55DAP/53DAP	1.03884	0.911
57DAP/55DAP	1.15011	0.71
62DAP/57DAP	0.95844	0.162
68DAP/62DAP	1.00415	1
68DAP/14DAP	0.93901	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92882	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.46535	0.437
Immature Eggplant/Mature Eggplant	1.40305
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.01423

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.83922
1-1-2/M82	0.77264
12-2/M82	1.0227
12-4/M82	1.03675	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	N/A	N/A
3-2/M82	1.06402
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.68785
4-3/M82	N/A	N/A
5-3/M82	0.71302
6-2/M82	1.13694
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.65081	0.243
IL2-6/WTpooled	0.98082	1
IL7-5/WTpooled	1.69165	0.792
IL7-3/WTpooled	0.83697	1
IL12-4/WTpooled	0.7998	0.478
IL1-4/WTpooled	1.01341
WT/WTpooled	1.01864	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	1.26184

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00263	1
DC3000/delta hrp 6h	1.08006	1
DC3000/delta hrp 12h	0.96804	1
DC3000/delta hrp 24h	1.01677	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42052	0.11
DC3000 delta B/DC3000 delta AB	1.27271	0.159

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	1.02725	1
Var 0h	0.48667	0.261
Var 12h I row2-row1	1.07319	0.443
Var 12h NI row2-row1	0.85859	0.546
Var 36h I row2-row1	1.15121	1
Var 36h NI row2-row1	0.9416	0.645
Var 60h I row2-row1	1.34475	0.562
Var 60h NI row2-row1	1.36917	0.904
Time course 0hI-0hNI	1.14578	0.63
Time course 12hI-12hNI	0.9987	1
Time course 36hI-36hNI	0.96266	0.274
Time course 60hI-60hNI	1.13913	0.069

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)	0.95259	0.722
transgenic ySAMdc/azygous control (breaker)	1.52293	0.162
transgenic ySAMdc/azygous control (red)	1.08687	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99661	0.737

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15376	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.57265	0.172
Manapal/WT (break)	0.86528	1
Manapal/WT (red)	0.63204	0.216