Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60601	0.032
27DAP/17DAP	1.05358	0.994
39DAP/27DAP	1.11922	1
41DAP/39DAP	0.91169	0.632
42DAP/41DAP	0.50146	0.251
43DAP/42DAP	0.72836	0.546
47DAP/43DAP	0.61412	0.079
52DAP/47DAP	1.63565	0.227
57DAP/52DAP	0.92044	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95683	0.006
17DAP/reference	0.96486	0.63
27DAP/reference	0.79675	0.029
39DAP/reference	0.96068	0.513
41DAP/reference	0.95307	0.434
42DAP/reference	0.85352	0.029
43DAP/reference	0.80097	0.025
47DAP/reference	0.8339	0.042
52DAP/reference	0.79255	0.121
57DAP/reference	0.95529	0.324

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.41827	0.019
27DAP/17DAP	1.30644	0.108
39DAP/27DAP	0.7087	0.032
41DAP/39DAP	0.75361	0.117
42DAP/41DAP	1.05845	0.694
43DAP/42DAP	1.01446	1
47DAP/43DAP	0.72388	0.026
52DAP/47DAP	1.06295	0.915
57DAP/52DAP	0.98356	0.81
57DAP/7DAP	0.60481	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.94515	0.025
17DAP/reference	1.96437	0.01
27DAP/reference	1.29272	0.008
39DAP/reference	1.13418	0.391
41DAP/reference	1.66142	0.009
42DAP/reference	1.22175	0.059
43DAP/reference	1.27469	0.031
47DAP/reference	0.95674	0.504
52DAP/reference	1.05986	0.428
57DAP/reference	0.92255	0.156

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87608	0.029
17DAP/reference	1.40425	0.058
27DAP/reference	1.21098	0.1
39DAP/reference	1.00412	0.722
41DAP/reference	1.31893	0.012
42DAP/reference	1.10493	0.596
43DAP/reference	1.01472	0.801
47DAP/reference	1.29536	0.043
52DAP/reference	0.99335	0.619
57DAP/reference	0.97961	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58526	0.015
17DAP/reference	1.6621	0.111
27DAP/reference	1.68951	0.019
39DAP/reference	1.67325	0.009
41DAP/reference	1.41898	0.008
42DAP/reference	1.11056	0.391
43DAP/reference	0.93878	0.468
47DAP/reference	0.62351	0.006
52DAP/reference	1.15284	0.79
57DAP/reference	0.90129	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15805	1
26DAP/20DAP	1.63364
34DAP/26DAP	1.65204	0.542
51DAP/34DAP	0.97733	0.873
52DAP/51DAP	1.36308	0.225
53DAP/52DAP	0.78777	0.049
55DAP/53DAP	1.73976	0.375
57DAP/55DAP	1.24175	0.87
62DAP/57DAP	0.78324	0.05
68DAP/62DAP	0.98631	0.834
68DAP/14DAP	0.88904	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.91534	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.1285	0.015
Immature Eggplant/Mature Eggplant	1.35688	0.205
Ripe Pepper/Ripe Tomato	0.37612	0.293
Mature Eggplant/Ripe Tomato	0.89387

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.01465
1-3/M82	0.54614
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.08771	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.35701
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.00317	1
6-2/M82	N/A	N/A
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	1.00537

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02423
IL2-6/WTpooled	1.03131	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.99817	1
IL12-4/WTpooled	1.15359	0.546
IL1-4/WTpooled	1.01885	1
WT/WTpooled	0.98908	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	0.6258	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1094	0.921
DC3000/delta hrp 6h	0.89825	0.95
DC3000/delta hrp 12h	1.00274	1
DC3000/delta hrp 24h	1.04949	0.535

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.94398

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9889	1
Exp 36h	N/A	N/A
Exp 60h	0.96774	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00507	1
Var 0h	1.26324	0.936
Var 12h I row2-row1	0.61744	0.338
Var 12h NI row2-row1	0.96906	0.546
Var 36h I row2-row1	0.91631	0.805
Var 36h NI row2-row1	0.89263	0.45
Var 60h I row2-row1	1.16397	0.562
Var 60h NI row2-row1	0.92792	0.818
Time course 0hI-0hNI	1.03317	0.719
Time course 12hI-12hNI	0.91488	0.362
Time course 36hI-36hNI	0.81248	0.084
Time course 60hI-60hNI	0.56521	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)	0.77454	0.246
transgenic ySAMdc/azygous control (breaker)	0.64573	0.251
transgenic ySAMdc/azygous control (red)	1.04195	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97364	0.277

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.66871	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6865	0.172
Manapal/WT (break)	0.80862	1
Manapal/WT (red)	1.02934	1