Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.12.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.73094	0.037
27DAP/17DAP	0.5312	0.044
39DAP/27DAP	1.3133	0.473
41DAP/39DAP	1.0138	0.868
42DAP/41DAP	2.03609	0.138
43DAP/42DAP	1.84882	0.348
47DAP/43DAP	0.95702	0.828
52DAP/47DAP	0.51634	0.055
57DAP/52DAP	0.99853	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86773	0.075
17DAP/reference	0.66104	0.091
27DAP/reference	0.35348	0.011
39DAP/reference	0.87811	0.261
41DAP/reference	0.6319	0.021
42DAP/reference	2.0764	0.002
43DAP/reference	2.00189	0.008
47DAP/reference	2.22336	0.002
52DAP/reference	0.46866	0.02
57DAP/reference	0.53395	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.33041	0.017
27DAP/17DAP	0.9722	0.887
39DAP/27DAP	0.80751	0.121
41DAP/39DAP	1.09244	0.69
42DAP/41DAP	1.28396	0.075
43DAP/42DAP	1.67903	0.028
47DAP/43DAP	1.33162	0.133
52DAP/47DAP	1.42426	0.237
57DAP/52DAP	0.68642	0.15
57DAP/7DAP	0.43062	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28035	0.07
17DAP/reference	1.17316	0.147
27DAP/reference	1.04941	1
39DAP/reference	1.02632	0.64
41DAP/reference	1.68077	0.013
42DAP/reference	1.20377	0.1
43DAP/reference	1.37721	0.074
47DAP/reference	1.02422	0.868
52DAP/reference	0.75745	0.027
57DAP/reference	0.7469	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42728	0.315
17DAP/reference	1.96445	0.009
27DAP/reference	1.18878	0.686
39DAP/reference	0.72013	0.105
41DAP/reference	2.93499	0.005
42DAP/reference	0.88967	0.135
43DAP/reference	0.89175	0.236
47DAP/reference	1.57184	0.033
52DAP/reference	0.71331	0.016
57DAP/reference	0.82005	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0763	0.984
17DAP/reference	1.16045	0.792
27DAP/reference	0.81879	0.126
39DAP/reference	0.98082	0.591
41DAP/reference	0.95346	0.512
42DAP/reference	2.25606	0.347
43DAP/reference	3.16936	0.047
47DAP/reference	3.37566	0.007
52DAP/reference	1.71932	0.073
57DAP/reference	1.12059	0.947

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87727	1
26DAP/20DAP	0.87817	0.512
34DAP/26DAP	1.21078	1
51DAP/34DAP	1.76444	0.511
52DAP/51DAP	1.47964	0.035
53DAP/52DAP	1.16431	0.753
55DAP/53DAP	1.36747	0.046
57DAP/55DAP	1.04974	0.975
62DAP/57DAP	0.34358	0.016
68DAP/62DAP	0.80151	0.464
68DAP/14DAP	0.5856	0.056

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.02024	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.12119	0.058
Mature Green Tomato/Ripe Tomato	0.88742	0.611
Immature Eggplant/Mature Eggplant	0.44582	0.062
Ripe Pepper/Ripe Tomato	0.19571	0.224
Mature Eggplant/Ripe Tomato	0.12103	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	3.27022	0.591
1-1-2/M82	2.48132	1
12-2/M82	0.98752	1
12-4/M82	3.69232	1
1-3/M82	2.55513	0.26
2-1-1/M82	0.83628	0.465
2-1/M82	1.00752	1
2-6/M82	1.06867	1
3-2/M82	1.08079	0.549
4-1-1/M82	1.17979	1
4-1/M82	6.3195	1
4-3-2/M82	1.40826	0.508
4-3/M82	0.94753	1
5-3/M82	0.94915	1
6-2/M82	1.76384	0.253
6-3/M82	0.87467	1
7-1/M82	0.88791	1
7-2/M82	0.54754	0.553
9-3-2/M82	2.3252	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75225
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.70981	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98594	1
DC3000/delta hrp 6h	1.2603	1
DC3000/delta hrp 12h	0.65722	1
DC3000/delta hrp 24h	0.95723	0.782

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.65721	0.042
DC3000 delta B/DC3000 delta AB	1.34398	0.133

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91217	1
Exp 36h	0.61352	0.456
Exp 60h	0.56369	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97784	1
Var 0h	0.89793	1
Var 12h I row2-row1	0.77036	0.467
Var 12h NI row2-row1	0.94458	0.546
Var 36h I row2-row1	0.89402	1
Var 36h NI row2-row1	1.08873	1
Var 60h I row2-row1	0.84151	0.832
Var 60h NI row2-row1	1.00628	1
Time course 0hI-0hNI	0.97731	0.906
Time course 12hI-12hNI	0.94943	0.338
Time course 36hI-36hNI	0.84678	0.041
Time course 60hI-60hNI	0.47257	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)	0.8695	0.237
transgenic ySAMdc/azygous control (breaker)	0.49714	0.139
transgenic ySAMdc/azygous control (red)	1.01672	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7974	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.22745	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84452	1
Manapal/WT (break)	0.80954	0.333
Manapal/WT (red)	0.45003	0.187