Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99521	0.811
27DAP/17DAP	1.12264	0.866
39DAP/27DAP	0.85648	0.583
41DAP/39DAP	0.98271	0.825
42DAP/41DAP	1.24851	0.899
43DAP/42DAP	0.95382	0.909
47DAP/43DAP	1.2088	0.618
52DAP/47DAP	0.94255	0.812
57DAP/52DAP	0.99287	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01767	1
17DAP/reference	1.15481	0.04
27DAP/reference	0.99029	0.741
39DAP/reference	1.12726	0.174
41DAP/reference	1.23086	0.102
42DAP/reference	0.88566	0.028
43DAP/reference	1.00824	1
47DAP/reference	0.90667	0.06
52DAP/reference	0.77828	0.038
57DAP/reference	0.8136	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95954	0.613
27DAP/17DAP	1.07353	0.751
39DAP/27DAP	1.17351	0.383
41DAP/39DAP	0.99387	0.997
42DAP/41DAP	0.89981	0.279
43DAP/42DAP	1.12529	0.086
47DAP/43DAP	0.96982	0.87
52DAP/47DAP	1.03456	0.927
57DAP/52DAP	0.9411	0.587
57DAP/7DAP	1.3311

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.893	0.27
17DAP/reference	1.09154	0.269
27DAP/reference	1.03476	0.551
39DAP/reference	1.18767	0.57
41DAP/reference	0.95235	0.247
42DAP/reference	1.01879	0.828
43DAP/reference	1.19372	0.256
47DAP/reference	0.99489	1
52DAP/reference	0.97484	0.477
57DAP/reference	1.1343	0.061

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12565	0.337
17DAP/reference	1.05631	0.69
27DAP/reference	0.95956	0.467
39DAP/reference	0.96423	0.416
41DAP/reference	0.82401	0.04
42DAP/reference	0.81273	0.014
43DAP/reference	1.37977	0.082
47DAP/reference	0.84967	0.054
52DAP/reference	0.98096	0.469
57DAP/reference	1.24709	0.146

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96912	0.526
17DAP/reference	1.28516	0.572
27DAP/reference	1.2529	0.096
39DAP/reference	1.01046	1
41DAP/reference	0.97899	0.618
42DAP/reference	1.04747	0.923
43DAP/reference	0.83234	0.098
47DAP/reference	0.90756	0.109
52DAP/reference	2.91247	0.113
57DAP/reference	0.98371	0.353

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03618	0.966
26DAP/20DAP	0.84063	0.512
34DAP/26DAP	1.07315	1
51DAP/34DAP	0.90516	0.376
52DAP/51DAP	0.93705	1
53DAP/52DAP	1.35124	0.075
55DAP/53DAP	1.14031	0.177
57DAP/55DAP	1.13836	0.231
62DAP/57DAP	1.13271	0.678
68DAP/62DAP	0.68311	0.053
68DAP/14DAP	0.48689	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72674	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
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	1.10838
12-2/M82	1.04356	1
12-4/M82	1.19028
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	0.93418
3-2/M82	0.90624
4-1-1/M82	1.18294
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	1.13706
6-2/M82	0.74307
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	1.16962	0.277
IL2-6/WTpooled	1.09052	0.531
IL7-5/WTpooled	1.21664	1
IL7-3/WTpooled	1.14731	0.362
IL12-4/WTpooled	1.23654	0.516
IL1-4/WTpooled	0.87483	0.834
WT/WTpooled	0.95885	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	0.86991

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03435	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.17229	1
DC3000/delta hrp 24h	1.15926	0.158

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18087	0.183
DC3000 delta B/DC3000 delta AB	1.12185	0.571

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	1.08115	1
Var 0h	1.04389	0.594
Var 12h I row2-row1	1.0643	0.736
Var 12h NI row2-row1	1.07409	0.649
Var 36h I row2-row1	0.81321	0.805
Var 36h NI row2-row1	0.7021	0.522
Var 60h I row2-row1	0.95652	1
Var 60h NI row2-row1	1.25238	0.904
Time course 0hI-0hNI	0.95694	0.801
Time course 12hI-12hNI	0.96421	0.802
Time course 36hI-36hNI	0.80702	0.023
Time course 60hI-60hNI	0.94377	0.646

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.32978	0.139
transgenic ySAMdc/azygous control (red)	0.79668	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00903	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80944	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.52385	0.093
Manapal/WT (break)	1.93097	0.183
Manapal/WT (red)	1.24544	0.413