Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.19.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09932	0.938
27DAP/17DAP	0.9311	0.791
39DAP/27DAP	4.9353	0.02
41DAP/39DAP	2.39386	0.202
42DAP/41DAP	3.88081	0.021
43DAP/42DAP	2.36919	0.778
47DAP/43DAP	0.92447	0.701
52DAP/47DAP	0.53085	0.107
57DAP/52DAP	1.54707	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68551	0.074
17DAP/reference	0.57724	0.015
27DAP/reference	0.95024	0.654
39DAP/reference	1.16161	1
41DAP/reference	1.18806	0.241
42DAP/reference	4.04332	0.001
43DAP/reference	2.92801	0.866
47DAP/reference	3.23626	0.005
52DAP/reference	1.665	0.007
57DAP/reference	1.14816

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.49133	0.031
27DAP/17DAP	1.41754	0.061
39DAP/27DAP	2.73594	0.037
41DAP/39DAP	0.30657	0.013
42DAP/41DAP	2.97969	0.002
43DAP/42DAP	4.20259	0.013
47DAP/43DAP	0.85967	0.41
52DAP/47DAP	1.01326	0.919
57DAP/52DAP	1.35642	0.215
57DAP/7DAP	2.13074	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01242	1
17DAP/reference	0.96977	0.447
27DAP/reference	0.77057	0.048
39DAP/reference	1.05817	0.909
41DAP/reference	1.04336	0.778
42DAP/reference	1.07322	0.686
43DAP/reference	1.1213	0.788
47DAP/reference	1.58723	0.062
52DAP/reference	1.27962	0.014
57DAP/reference	1.10399	0.147

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5782	0.051
17DAP/reference	0.43913	0.004
27DAP/reference	0.56598	0.03
39DAP/reference	0.63537	0.008
41DAP/reference	0.56543	0.009
42DAP/reference	0.67903	0.046
43DAP/reference	0.97206	0.569
47DAP/reference	0.80229	0.071
52DAP/reference	0.5589	0.005
57DAP/reference	0.65446	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00927	0.699
17DAP/reference	0.78487	0.374
27DAP/reference	0.97123	0.624
39DAP/reference	0.97001	0.504
41DAP/reference	1.08576	0.605
42DAP/reference	1.26639	0.084
43DAP/reference	2.9631	0.018
47DAP/reference	3.516	0.005
52DAP/reference	1.25178	0.212
57DAP/reference	1.19837	0.462

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.75167	0.807
26DAP/20DAP	0.94999	1
34DAP/26DAP	1.01298	1
51DAP/34DAP	0.64639	0.058
52DAP/51DAP	1.11492	0.404
53DAP/52DAP	0.77398	0.049
55DAP/53DAP	0.61973	0.021
57DAP/55DAP	0.85073	0.351
62DAP/57DAP	1.34695	0.569
68DAP/62DAP	1.20671	0.657
68DAP/14DAP	0.57088

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.05036	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.19634	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.2176	0.293
Mature Eggplant/Ripe Tomato	0.03386	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09033	0.877
1-1-2/M82	1.10148	1
12-2/M82	0.81983	0.955
12-4/M82	0.97235	1
1-3/M82	2.22259	0.277
2-1-1/M82	0.80931	0.465
2-1/M82	0.97463	1
2-6/M82	0.92987	1
3-2/M82	1.07763	0.717
4-1-1/M82	0.91829	1
4-1/M82	0.83708
4-3-2/M82	0.81563
4-3/M82	0.86836	0.72
5-3/M82	0.91503	1
6-2/M82	1.00319	1
6-3/M82	1.03329	1
7-1/M82	0.847	0.509
7-2/M82	0.9981	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.42608
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.49645	1
IL7-3/WTpooled	0.33595
IL12-4/WTpooled	0.57858
IL1-4/WTpooled	0.91043	0.834
WT/WTpooled	0.91853

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	0.81793	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97827	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.61719
DC3000/delta hrp 24h	0.63046	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50983	0.023
DC3000 delta B/DC3000 delta AB	0.54653	0.02

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	1.04837	1
Var 0h	1.18299	0.421
Var 12h I row2-row1	0.83659	0.338
Var 12h NI row2-row1	0.93134	0.82
Var 36h I row2-row1	0.70498	1
Var 36h NI row2-row1	1.37474	0.482
Var 60h I row2-row1	0.89645	0.582
Var 60h NI row2-row1	0.93774	1
Time course 0hI-0hNI	1.01294	0.852
Time course 12hI-12hNI	0.94084	0.54
Time course 36hI-36hNI	0.8206	0.023
Time course 60hI-60hNI	0.18551	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)	0.64103	0.391
transgenic ySAMdc/azygous control (breaker)	1.04795	1
transgenic ySAMdc/azygous control (red)	0.99318	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26868	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74118	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.8545	0.242