Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-7.4.16.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88472	0.278
27DAP/17DAP	1.03887	0.922
39DAP/27DAP	0.93736	0.641
41DAP/39DAP	1.08075	0.844
42DAP/41DAP	0.91964	1
43DAP/42DAP	1.05043	1
47DAP/43DAP	1.15167	0.542
52DAP/47DAP	0.89092	0.683
57DAP/52DAP	1.07476	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05525	0.241
17DAP/reference	0.91155	0.069
27DAP/reference	0.95869	0.406
39DAP/reference	0.91751	0.174
41DAP/reference	0.84908	0.039
42DAP/reference	1.05561	0.21
43DAP/reference	0.92857	0.118
47DAP/reference	1.05597	0.685
52DAP/reference	1.14099	0.065
57DAP/reference	1.15986	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84617	0.164
27DAP/17DAP	1.10959	0.754
39DAP/27DAP	0.79469	0.105
41DAP/39DAP	0.83039	0.372
42DAP/41DAP	1.10793	0.708
43DAP/42DAP	1.16075	0.212
47DAP/43DAP	0.96383	0.833
52DAP/47DAP	1.08239	0.804
57DAP/52DAP	1.1459	0.451
57DAP/7DAP	0.97366	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12309	0.472
17DAP/reference	0.97746	0.518
27DAP/reference	0.91705	0.303
39DAP/reference	0.96327	0.411
41DAP/reference	0.96379	0.449
42DAP/reference	0.8854	0.07
43DAP/reference	1.12006	0.307
47DAP/reference	1.16423	0.191
52DAP/reference	1.27055	0.048
57DAP/reference	1.16498	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03071	0.724
17DAP/reference	1.02123	0.806
27DAP/reference	1.16847	0.139
39DAP/reference	1.14351	0.29
41DAP/reference	1.21418	0.078
42DAP/reference	1.09113	0.214
43DAP/reference	0.8733	0.087
47DAP/reference	0.91674	0.094
52DAP/reference	0.98388	0.5
57DAP/reference	0.94351	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96227	0.566
17DAP/reference	0.96692	0.579
27DAP/reference	0.98971	0.727
39DAP/reference	1.00542	1
41DAP/reference	1.08218	0.674
42DAP/reference	1.02173	1
43DAP/reference	1.16138	0.241
47DAP/reference	0.99572	0.626
52DAP/reference	1.07482	0.601
57DAP/reference	1.77462	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18017	0.878
26DAP/20DAP	1.40664	0.338
34DAP/26DAP	0.84792	0.61
51DAP/34DAP	1.30954	0.192
52DAP/51DAP	0.92616	1
53DAP/52DAP	0.75193	0.106
55DAP/53DAP	0.82176	0.195
57DAP/55DAP	1.02543	0.899
62DAP/57DAP	0.91699	0.871
68DAP/62DAP	1.127	0.845
68DAP/14DAP	1.22381	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01504	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.73701	0.059
Mature Green Tomato/Ripe Tomato	1.57387	0.299
Immature Eggplant/Mature Eggplant	0.71436	0.092
Ripe Pepper/Ripe Tomato	0.64072	0.224
Mature Eggplant/Ripe Tomato	2.80694	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94314	N/A
1-1-2/M82	0.74478	0.804
12-2/M82	N/A	N/A
12-4/M82	1.20865	0.694
1-3/M82	N/A	N/A
2-1-1/M82	0.96168	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.97604	1
4-1-1/M82	N/A	N/A
4-1/M82	0.84902	N/A
4-3-2/M82	1.04866	0.508
4-3/M82	N/A	N/A
5-3/M82	1.03176	1
6-2/M82	N/A	N/A
6-3/M82	1.16057	N/A
7-1/M82	0.78169	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.09204	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.96921	1
IL7-5/WTpooled	1.13225	N/A
IL7-3/WTpooled	0.81435	1
IL12-4/WTpooled	0.97169	1
IL1-4/WTpooled	0.93293	N/A
WT/WTpooled	0.90543	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	1.10401	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02022	1
DC3000/delta hrp 6h	1.05752	1
DC3000/delta hrp 12h	1.23215	1
DC3000/delta hrp 24h	0.84822	0.155

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06576	0.441
DC3000 delta B/DC3000 delta AB	1.01564	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.85514	1
Exp 36h	1.07821	1
Exp 60h	0.99978	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02103	1
Var 0h	0.99138	1
Var 12h I row2-row1	1.24214	0.506
Var 12h NI row2-row1	1.18076	0.34
Var 36h I row2-row1	0.97228	1
Var 36h NI row2-row1	1.36025	1
Var 60h I row2-row1	0.75825	0.285
Var 60h NI row2-row1	1.07721	1
Time course 0hI-0hNI	0.9539	0.763
Time course 12hI-12hNI	0.99853	1
Time course 36hI-36hNI	0.9034	0.206
Time course 60hI-60hNI	1.39262	0.053

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)	1.1021	0.511
transgenic ySAMdc/azygous control (breaker)	0.7492	0.15
transgenic ySAMdc/azygous control (red)	1.11562	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96885	0.231

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80052	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08098	1
Manapal/WT (break)	1.65298	0.183
Manapal/WT (red)	1.09582	1