Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32919	0.224
27DAP/17DAP	0.89511	0.8
39DAP/27DAP	0.70519	0.226
41DAP/39DAP	1.44667	0.288
42DAP/41DAP	1.20237	0.702
43DAP/42DAP	0.89602	0.807
47DAP/43DAP	1.86947	0.261
52DAP/47DAP	1.13883	0.96
57DAP/52DAP	1.33879	0.748

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86669	0.128
17DAP/reference	0.98003	0.819
27DAP/reference	0.97597	0.763
39DAP/reference	0.91304	0.06
41DAP/reference	0.77438	0.341
42DAP/reference	0.51566	0.001
43DAP/reference	0.64034	0.48
47DAP/reference	0.81734	0.077
52DAP/reference	0.81189
57DAP/reference	1.1647	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87694	0.376
27DAP/17DAP	1.08743	0.951
39DAP/27DAP	1.10391	0.565
41DAP/39DAP	0.73893	0.083
42DAP/41DAP	1.2729	0.012
43DAP/42DAP	1.22047	0.086
47DAP/43DAP	0.90929	0.606
52DAP/47DAP	0.93135	0.778
57DAP/52DAP	0.70781	0.103
57DAP/7DAP	1.42484	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20628	0.263
17DAP/reference	1.11392	0.477
27DAP/reference	1.12252	0.301
39DAP/reference	1.28505	0.016
41DAP/reference	1.3487	0.022
42DAP/reference	1.20693	0.405
43DAP/reference	1.25926	0.074
47DAP/reference	0.7612	0.03
52DAP/reference	1.23994	0.086
57DAP/reference	1.214	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91301	0.286
17DAP/reference	0.77422	0.056
27DAP/reference	1.09537	0.692
39DAP/reference	1.21097	0.401
41DAP/reference	1.21941	0.309
42DAP/reference	0.99311	0.655
43DAP/reference	0.90429	0.336
47DAP/reference	0.87251	0.069
52DAP/reference	1.10249	0.208
57DAP/reference	1.16068	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99185	0.607
17DAP/reference	0.93567	0.508
27DAP/reference	1.09322	0.834
39DAP/reference	1.13579	0.496
41DAP/reference	1.17192	0.486
42DAP/reference	1.38462	0.094
43DAP/reference	1.39831	0.098
47DAP/reference	0.84183	0.286
52DAP/reference	1.41783	0.1
57DAP/reference	1.34076	0.041

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05175	1
26DAP/20DAP	0.67196
34DAP/26DAP	1.23293	1
51DAP/34DAP	1.0941	0.814
52DAP/51DAP	0.6374	1
53DAP/52DAP	1.02796	0.998
55DAP/53DAP	0.99746	0.908
57DAP/55DAP	1.26811	0.764
62DAP/57DAP	1.21136	0.902
68DAP/62DAP	1.01658	1
68DAP/14DAP	1.43339	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.34413	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.968	0.591
Mature Green Tomato/Ripe Tomato	0.67234	0.06
Immature Eggplant/Mature Eggplant	1.41042	0.07
Ripe Pepper/Ripe Tomato	0.44231	0.224
Mature Eggplant/Ripe Tomato	0.72914	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12768	0.742
1-1-2/M82	1.00639	1
12-2/M82	1.13868	0.61
12-4/M82	1.18181
1-3/M82	0.86748
2-1-1/M82	0.92071	1
2-1/M82	N/A	N/A
2-6/M82	0.82737
3-2/M82	N/A	N/A
4-1-1/M82	0.83393	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.19917	0.268
5-3/M82	1.02079	1
6-2/M82	1.37894
6-3/M82	1.02603	1
7-1/M82	0.97089
7-2/M82	1.09347	0.385
9-3-2/M82	0.81161

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.46914	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.24866	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.75874	0.415
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	1.01767	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03952	0.921
DC3000/delta hrp 6h	1.11882	1
DC3000/delta hrp 12h	0.9368	1
DC3000/delta hrp 24h	1.22977	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.08721

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86756	1
Exp 36h	1.15438	0.409
Exp 60h	1.31157	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97874	1
Var 0h	0.65769	0.933
Var 12h I row2-row1	1.14595	0.296
Var 12h NI row2-row1	0.86572	0.713
Var 36h I row2-row1	0.94329	1
Var 36h NI row2-row1	1.22218	1
Var 60h I row2-row1	0.89122	0.285
Var 60h NI row2-row1	1.17111	0.904
Time course 0hI-0hNI	0.90053	0.329
Time course 12hI-12hNI	0.90021	0.188
Time course 36hI-36hNI	0.69028	0.023
Time course 60hI-60hNI	0.32005	0.006

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)	0.97962	0.662
transgenic ySAMdc/azygous control (breaker)	1.04466	0.248
transgenic ySAMdc/azygous control (red)	1.11254	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.87433	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16823	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93467	1
Manapal/WT (break)	0.95382	1
Manapal/WT (red)	0.90661	0.274