Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.4.7.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99278	0.788
27DAP/17DAP	1.10256	0.857
39DAP/27DAP	0.88696	0.462
41DAP/39DAP	0.73504	0.185
42DAP/41DAP	1.17434	0.877
43DAP/42DAP	0.96868	0.91
47DAP/43DAP	1.2119	0.203
52DAP/47DAP	0.88147	0.651
57DAP/52DAP	0.9807	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89701	0.058
17DAP/reference	1.1801	0.016
27DAP/reference	1.08389	0.132
39DAP/reference	1.06898	0.393
41DAP/reference	1.09395	0.187
42DAP/reference	0.88587	0.013
43DAP/reference	1.03722	0.705
47DAP/reference	0.91134	0.09
52DAP/reference	0.9225	0.089
57DAP/reference	0.95531	0.415

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96447	0.663
27DAP/17DAP	0.88364	0.724
39DAP/27DAP	1.35925	0.063
41DAP/39DAP	0.99065	1
42DAP/41DAP	0.97364	0.787
43DAP/42DAP	1.13629	0.273
47DAP/43DAP	0.98145	0.947
52DAP/47DAP	1.10559	0.63
57DAP/52DAP	0.80558	0.201
57DAP/7DAP	0.95337	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81261	0.088
17DAP/reference	1.08879	0.297
27DAP/reference	0.9644	0.43
39DAP/reference	0.63433	0.027
41DAP/reference	0.54199	0.017
42DAP/reference	0.53239	0.01
43DAP/reference	0.76226	0.034
47DAP/reference	0.85505	0.057
52DAP/reference	0.89414	0.066
57DAP/reference	0.93445	0.109

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01438	0.907
17DAP/reference	1.02345	0.892
27DAP/reference	0.87425	0.115
39DAP/reference	0.9251	0.298
41DAP/reference	0.91374	0.237
42DAP/reference	0.9153	0.03
43DAP/reference	1.22358	0.211
47DAP/reference	0.94737	0.221
52DAP/reference	0.94579	0.38
57DAP/reference	1.08067	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85206	0.169
17DAP/reference	0.93807	0.335
27DAP/reference	0.85262	0.085
39DAP/reference	1.08911	0.563
41DAP/reference	0.85797	0.132
42DAP/reference	0.82879	0.108
43DAP/reference	0.74765	0.033
47DAP/reference	1.06758	0.251
52DAP/reference	1.07779	0.89
57DAP/reference	0.80707	0.129

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03614	0.966
26DAP/20DAP	0.94654	1
34DAP/26DAP	1.13177	0.819
51DAP/34DAP	1.32695	0.314
52DAP/51DAP	0.89411	1
53DAP/52DAP	1.10155	0.753
55DAP/53DAP	1.509	0.79
57DAP/55DAP	1.03655	0.986
62DAP/57DAP	1.01688	1
68DAP/62DAP	0.83851	0.429
68DAP/14DAP	0.72312	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99401	0.547

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.55429	0.299
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	1.30946	0.473
1-1-2/M82	1.06654	1
12-2/M82	0.80004	0.955
12-4/M82	1.19007	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.65281	N/A
2-6/M82	N/A	N/A
3-2/M82	1.1121	0.967
4-1-1/M82	0.85369	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.16634	N/A
5-3/M82	1.03542	0.572
6-2/M82	1.19177	N/A
6-3/M82	0.96047	1
7-1/M82	0.97007	N/A
7-2/M82	1.0266	1
9-3-2/M82	1.17947	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.77881	N/A
IL2-6/WTpooled	0.73737	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03268	1
IL12-4/WTpooled	1.00325	1
IL1-4/WTpooled	1.00623	N/A
WT/WTpooled	0.9398	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	1.0939	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03701	0.921
DC3000/delta hrp 6h	1.16833	1
DC3000/delta hrp 12h	1.14943	1
DC3000/delta hrp 24h	1.04597	0.633

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85479	1
Exp 36h	0.65505	0.749
Exp 60h	0.83682	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.13229	N/A
Var 0h	1.48071	0.311
Var 12h I row2-row1	1.17442	0.272
Var 12h NI row2-row1	0.90329	0.713
Var 36h I row2-row1	1.0972	1
Var 36h NI row2-row1	1.20576	1
Var 60h I row2-row1	1.20719	0.562
Var 60h NI row2-row1	1.05134	1
Time course 0hI-0hNI	0.98349	0.967
Time course 12hI-12hNI	0.93952	0.711
Time course 36hI-36hNI	0.91841	0.23
Time course 60hI-60hNI	0.88484	0.081

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)	0.82707	0.299
transgenic ySAMdc/azygous control (breaker)	1.04827	1
transgenic ySAMdc/azygous control (red)	1.0416	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98004	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68708	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20169	1
Manapal/WT (break)	1.09444	1
Manapal/WT (red)	1.05124	1