Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01589	0.938
27DAP/17DAP	0.91532	0.819
39DAP/27DAP	0.83759	0.335
41DAP/39DAP	1.05447	0.929
42DAP/41DAP	1.09525	0.974
43DAP/42DAP	1.05503	1
47DAP/43DAP	0.84947	0.522
52DAP/47DAP	1.0881	0.967
57DAP/52DAP	0.93422	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07203	0.188
17DAP/reference	1.02296	0.653
27DAP/reference	0.92456	0.098
39DAP/reference	0.96425	0.475
41DAP/reference	0.96227	0.434
42DAP/reference	0.94879	0.188
43DAP/reference	0.99829	0.904
47DAP/reference	0.85622	0.004
52DAP/reference	0.75655	0.014
57DAP/reference	0.85611	0.074

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14247	0.464
27DAP/17DAP	1.01571	0.973
39DAP/27DAP	0.80785	0.316
41DAP/39DAP	1.11981	0.623
42DAP/41DAP	0.8273	0.052
43DAP/42DAP	0.89696	0.367
47DAP/43DAP	1.00483	1
52DAP/47DAP	1.01819	0.982
57DAP/52DAP	0.90983	0.43
57DAP/7DAP	0.88025	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98728	0.613
17DAP/reference	0.86075	0.028
27DAP/reference	0.80847	0.02
39DAP/reference	0.8178	0.011
41DAP/reference	0.83572	0.019
42DAP/reference	0.77921	0.016
43DAP/reference	0.76431	0.013
47DAP/reference	0.7306	0.034
52DAP/reference	0.76722	0.01
57DAP/reference	0.76734	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01943	0.812
17DAP/reference	1.08105	0.471
27DAP/reference	0.96028	0.34
39DAP/reference	0.97501	0.509
41DAP/reference	0.99802	0.649
42DAP/reference	0.83323	0.011
43DAP/reference	0.97951	0.633
47DAP/reference	0.86791	0.014
52DAP/reference	0.95143	0.259
57DAP/reference	1.06673	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97296	0.526
17DAP/reference	1.12236	0.427
27DAP/reference	0.78108	0.031
39DAP/reference	0.87673	0.076
41DAP/reference	0.79174	0.024
42DAP/reference	0.69802	0.019
43DAP/reference	0.78867	0.022
47DAP/reference	0.87894	0.025
52DAP/reference	0.66575	0.091
57DAP/reference	0.64182	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33177	0.586
26DAP/20DAP	0.97632	1
34DAP/26DAP	0.98528	0.988
51DAP/34DAP	0.94816	0.688
52DAP/51DAP	1.03999	0.742
53DAP/52DAP	1.05165	0.91
55DAP/53DAP	1.12027	0.848
57DAP/55DAP	1.12455	0.764
62DAP/57DAP	0.99801	1
68DAP/62DAP	0.92133	0.641
68DAP/14DAP	0.87691	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06031	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.09771	0.058
Mature Green Tomato/Ripe Tomato	3.65067	0.015
Immature Eggplant/Mature Eggplant	0.67542	0.064
Ripe Pepper/Ripe Tomato	1.88253	1
Mature Eggplant/Ripe Tomato	15.2304	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90945
1-1-2/M82	0.89612	1
12-2/M82	0.90576	0.955
12-4/M82	1.13425	1
1-3/M82	0.73201	0.378
2-1-1/M82	1.06394
2-1/M82	N/A	N/A
2-6/M82	1.3052	0.395
3-2/M82	N/A	N/A
4-1-1/M82	1.12969	0.977
4-1/M82	N/A	N/A
4-3-2/M82	1.05949
4-3/M82	0.70669
5-3/M82	0.91054	0.642
6-2/M82	1.01076	1
6-3/M82	1.18606	1
7-1/M82	0.88255
7-2/M82	1.01147	1
9-3-2/M82	1.03598	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98765	1
IL2-6/WTpooled	0.94262	1
IL7-5/WTpooled	0.69283	1
IL7-3/WTpooled	0.82048	0.31
IL12-4/WTpooled	0.80579	0.581
IL1-4/WTpooled	0.95364	1
WT/WTpooled	0.94922	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	1.1998	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99356
DC3000/delta hrp 6h	0.85809	0.95
DC3000/delta hrp 12h	1.14823	1
DC3000/delta hrp 24h	0.57459	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.84176	0.46
DC3000 delta B/DC3000 delta AB	0.6523	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86801	0.328
Exp 36h	0.76105	0.334
Exp 60h	0.67122	0.257

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	0.8554	0.933
Var 12h I row2-row1	0.8231	0.338
Var 12h NI row2-row1	1.07043	1
Var 36h I row2-row1	1.19809	1
Var 36h NI row2-row1	1.67928	0.482
Var 60h I row2-row1	0.98607	1
Var 60h NI row2-row1	1.18676	0.904
Time course 0hI-0hNI	1.06586	0.764
Time course 12hI-12hNI	0.99472	0.984
Time course 36hI-36hNI	0.7752	0.029
Time course 60hI-60hNI	0.20781	0.005

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)	1.21783	0.339
transgenic ySAMdc/azygous control (breaker)	1.48975	0.248
transgenic ySAMdc/azygous control (red)	1.56508	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00277	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.50974	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.61483	0.086
Manapal/WT (break)	5.74295	0.123
Manapal/WT (red)	4.87116	0.137