Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01619	0.997
27DAP/17DAP	0.84859	0.73
39DAP/27DAP	1.67113	0.159
41DAP/39DAP	1.23809	0.451
42DAP/41DAP	0.92109	1
43DAP/42DAP	0.8903	0.829
47DAP/43DAP	0.74673	0.276
52DAP/47DAP	1.55071	0.528
57DAP/52DAP	1.27617	0.93

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.5893	0.017
17DAP/reference	0.46139	0.008
27DAP/reference	0.67187	0.024
39DAP/reference	0.5016	0.007
41DAP/reference	0.40351	0.008
42DAP/reference	0.63552	0.001
43DAP/reference	0.60958
47DAP/reference	0.77686	0.106
52DAP/reference	1.05725	0.576
57DAP/reference	0.47947

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95753	0.484
27DAP/17DAP	0.96812	0.475
39DAP/27DAP	0.94751	0.759
41DAP/39DAP	1.01179	0.921
42DAP/41DAP	0.97235	0.732
43DAP/42DAP	1.02916	0.446
47DAP/43DAP	1.00752	0.969
52DAP/47DAP	0.97928	0.902
57DAP/52DAP	1.03278	0.832
57DAP/7DAP	1.05937	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48567	0.036
17DAP/reference	1.61168	0.008
27DAP/reference	1.28204	0.008
39DAP/reference	1.39255	0.059
41DAP/reference	1.36838	0.041
42DAP/reference	1.40673	0.011
43DAP/reference	1.27466	0.063
47DAP/reference	1.08015	0.247
52DAP/reference	1.23452	0.055
57DAP/reference	1.21386	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68417	0.115
17DAP/reference	0.66166	0.043
27DAP/reference	0.78139	0.097
39DAP/reference	1.03724	0.661
41DAP/reference	0.95084	0.322
42DAP/reference	0.93264	0.355
43DAP/reference	0.57382	0.026
47DAP/reference	0.74891	0.012
52DAP/reference	0.80921	0.101
57DAP/reference	0.47777	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45411	0.109
17DAP/reference	1.07808	0.934
27DAP/reference	1.1679	0.096
39DAP/reference	0.97607	0.544
41DAP/reference	1.11074	0.197
42DAP/reference	1.27374	0.108
43DAP/reference	1.16049	0.134
47DAP/reference	0.96563	0.452
52DAP/reference	1.49491	0.499
57DAP/reference	2.05347	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96728	1
26DAP/20DAP	0.94399	1
34DAP/26DAP	0.9185	0.44
51DAP/34DAP	1.00035	0.98
52DAP/51DAP	1.0839	0.295
53DAP/52DAP	1.00096	1
55DAP/53DAP	0.94194	0.515
57DAP/55DAP	0.91007	0.577
62DAP/57DAP	1.22358	0.303
68DAP/62DAP	3.01224	0.033
68DAP/14DAP	5.03189	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76773	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.59542	0.13
Mature Green Tomato/Ripe Tomato	0.65433	0.2
Immature Eggplant/Mature Eggplant	6.21744	0.321
Ripe Pepper/Ripe Tomato	3.34529
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99471	1
IL2-6/WTpooled	1.06995	0.788
IL7-5/WTpooled	1.10019
IL7-3/WTpooled	1.00207
IL12-4/WTpooled	0.94904	1
IL1-4/WTpooled	1.29925	1
WT/WTpooled	0.91009	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	1.00378	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00723	1
DC3000/delta hrp 6h	1.1441	0.978
DC3000/delta hrp 12h	0.81182	1
DC3000/delta hrp 24h	1.40445	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20436	0.11
DC3000 delta B/DC3000 delta AB	1.06318	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7674	1
Exp 36h	0.70096	0.449
Exp 60h	0.65398	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97423	1
Var 0h	0.90185	0.933
Var 12h I row2-row1	0.87603
Var 12h NI row2-row1	1.08245
Var 36h I row2-row1	1.19429	0.305
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.97474	0.911
Time course 12hI-12hNI	0.94848	0.745
Time course 36hI-36hNI	1.23414	0.009
Time course 60hI-60hNI	1.55168	0.008

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)	1.10572	0.272
transgenic ySAMdc/azygous control (breaker)	0.86568	0.49
transgenic ySAMdc/azygous control (red)	1.29821	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98872	0.552

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.76691	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.3017	0.083
Manapal/WT (break)	2.3918	0.183
Manapal/WT (red)	N/A	N/A