Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.13.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06637	0.893
27DAP/17DAP	1.06226	0.926
39DAP/27DAP	0.96028	0.663
41DAP/39DAP	1.19814	0.359
42DAP/41DAP	1.06302	1
43DAP/42DAP	0.96009	0.909
47DAP/43DAP	1.03777	0.904
52DAP/47DAP	1.29133	0.545
57DAP/52DAP	1.181	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00763	1
17DAP/reference	0.98535	0.664
27DAP/reference	0.97306	0.471
39DAP/reference	1.01517	0.889
41DAP/reference	1.01203	0.855
42DAP/reference	0.97855	0.188
43DAP/reference	0.99665	0.882
47DAP/reference	0.95892	0.083
52DAP/reference	0.96823	0.475
57DAP/reference	0.9402	0.051

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09225	0.581
27DAP/17DAP	1.04809	0.909
39DAP/27DAP	0.99611	1
41DAP/39DAP	1.08667	0.763
42DAP/41DAP	1.0262	0.947
43DAP/42DAP	1.00047	1
47DAP/43DAP	0.95852	0.63
52DAP/47DAP	0.99534	0.962
57DAP/52DAP	0.98868	0.813
57DAP/7DAP	0.99857	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91868	0.129
17DAP/reference	0.96734	0.025
27DAP/reference	1.11622	0.371
39DAP/reference	0.98866	0.23
41DAP/reference	0.9685	0.203
42DAP/reference	0.99214	0.675
43DAP/reference	0.92652	0.139
47DAP/reference	0.95957	0.383
52DAP/reference	0.93184	0.304
57DAP/reference	1.00932	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01565	0.741
17DAP/reference	0.95281	0.245
27DAP/reference	0.9472	0.317
39DAP/reference	1.01276	0.935
41DAP/reference	0.92293	0.089
42DAP/reference	0.9333	0.05
43DAP/reference	1.03883	0.874
47DAP/reference	0.94417	0.025
52DAP/reference	0.93054	0.06
57DAP/reference	1.02933	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98591	0.526
17DAP/reference	1.02589	0.757
27DAP/reference	0.96866	0.594
39DAP/reference	1.05539	0.163
41DAP/reference	0.98004	0.459
42DAP/reference	0.97664	0.671
43DAP/reference	0.91205	0.179
47DAP/reference	1.00889	1
52DAP/reference	1.09034	0.483
57DAP/reference	0.91597	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99223	1
26DAP/20DAP	0.98394	1
34DAP/26DAP	0.968	0.841
51DAP/34DAP	0.97276	0.747
52DAP/51DAP	0.97921	1
53DAP/52DAP	0.94485	0.684
55DAP/53DAP	0.95565	0.544
57DAP/55DAP	1.00309	1
62DAP/57DAP	0.94777	0.681
68DAP/62DAP	0.86621	0.609
68DAP/14DAP	0.93827	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05706	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13333	0.068
Mature Green Tomato/Ripe Tomato	0.81087	0.132
Immature Eggplant/Mature Eggplant	1.16308	0.363
Ripe Pepper/Ripe Tomato	0.53204	0.224
Mature Eggplant/Ripe Tomato	0.15994	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9905	0.961
1-1-2/M82	1.02513	1
12-2/M82	0.95802	0.955
12-4/M82	0.99688	1
1-3/M82	1.07374	0.479
2-1-1/M82	0.99404	1
2-1/M82	1.15875	1
2-6/M82	0.9857	1
3-2/M82	1.03611	0.463
4-1-1/M82	0.98496	1
4-1/M82	0.99133	1
4-3-2/M82	0.9065	0.487
4-3/M82	0.98338	1
5-3/M82	1.03155	1
6-2/M82	1.03817	1
6-3/M82	1.04488	1
7-1/M82	0.84653	1
7-2/M82	0.98542	1
9-3-2/M82	0.86688	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.16976
IL2-6/WTpooled	0.97192	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04852	1
IL12-4/WTpooled	1.00169	1
IL1-4/WTpooled	0.9882	1
WT/WTpooled	0.99606	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	0.94156	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08652	0.823
DC3000/delta hrp 6h	1.16184	1
DC3000/delta hrp 12h	0.93799	1
DC3000/delta hrp 24h	1.05493	0.567

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1584	0.042
DC3000 delta B/DC3000 delta AB	1.08091	0.443

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.87916	1
Exp 36h	1.13211	1
Exp 60h	1.2616	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98263	1
Var 0h	1.10003	0.98
Var 12h I row2-row1	1.24212	0.211
Var 12h NI row2-row1	1.03502	1
Var 36h I row2-row1	1.09581	1
Var 36h NI row2-row1	0.81365	0.61
Var 60h I row2-row1	1.17969	1
Var 60h NI row2-row1	1.05564	1
Time course 0hI-0hNI	1.04326	0.852
Time course 12hI-12hNI	1.0046	1
Time course 36hI-36hNI	0.99414	0.718
Time course 60hI-60hNI	1.33249	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)	0.84342	0.314
transgenic ySAMdc/azygous control (breaker)	1.63112	0.162
transgenic ySAMdc/azygous control (red)	0.99895	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06079	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19062	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6845	1
Manapal/WT (break)	0.9593	1
Manapal/WT (red)	1.19124	0.125