Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.3.8.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81217	0.211
27DAP/17DAP	1.24019	0.815
39DAP/27DAP	0.74703	0.392
41DAP/39DAP	1.21422	0.591
42DAP/41DAP	1.03133	1
43DAP/42DAP	1.10824	1
47DAP/43DAP	0.92057	0.687
52DAP/47DAP	1.17213	0.769
57DAP/52DAP	1.11045	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98524	0.616
17DAP/reference	0.9953	0.858
27DAP/reference	0.98315	0.694
39DAP/reference	1.1219	0.262
41DAP/reference	1.03287	0.855
42DAP/reference	1.03011	0.707
43DAP/reference	0.90602	0.273
47DAP/reference	1.2238	0.223
52DAP/reference	0.92467	0.237
57DAP/reference	1.00283	0.736

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8745	0.26
27DAP/17DAP	0.97784	0.748
39DAP/27DAP	1.00359	0.862
41DAP/39DAP	1.03758	0.781
42DAP/41DAP	1.03367	0.904
43DAP/42DAP	1.08716	0.072
47DAP/43DAP	1.0151	0.951
52DAP/47DAP	1.00791	0.986
57DAP/52DAP	1.01292	0.978
57DAP/7DAP	1.12112	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06948	0.793
17DAP/reference	1.22817	0.574
27DAP/reference	1.00445	0.8
39DAP/reference	1.07025	0.705
41DAP/reference	0.99376	0.677
42DAP/reference	1.01222	0.791
43DAP/reference	1.1935	0.307
47DAP/reference	0.93062	0.504
52DAP/reference	0.88425	0.022
57DAP/reference	1.11895	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41245	0.22
17DAP/reference	0.90302	0.317
27DAP/reference	1.07256	0.781
39DAP/reference	1.11111	0.62
41DAP/reference	0.90661	0.256
42DAP/reference	1.0607	1
43DAP/reference	1.36724	0.226
47DAP/reference	1.07538	0.454
52DAP/reference	0.99212	0.5
57DAP/reference	0.96962	0.61

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17481	0.329
17DAP/reference	1.05742	0.538
27DAP/reference	1.07455	0.447
39DAP/reference	1.03108	0.528
41DAP/reference	0.86886	0.237
42DAP/reference	0.71364	0.028
43DAP/reference	0.78648	0.052
47DAP/reference	1.00383	1
52DAP/reference	0.90833	0.464
57DAP/reference	0.87376	0.129

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93213	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.78385	N/A
51DAP/34DAP	0.92889	0.508
52DAP/51DAP	0.98923	1
53DAP/52DAP	1.07542	N/A
55DAP/53DAP	1.17145	N/A
57DAP/55DAP	1.07099	0.826
62DAP/57DAP	1.0165	1
68DAP/62DAP	0.88029	0.609
68DAP/14DAP	1.1734	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00059	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67586	0.212
Mature Green Tomato/Ripe Tomato	0.94306	0.522
Immature Eggplant/Mature Eggplant	2.07657	0.05
Ripe Pepper/Ripe Tomato	0.87756	1
Mature Eggplant/Ripe Tomato	0.92658	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95898	0.944
1-1-2/M82	1.14953	0.977
12-2/M82	1.01675	1
12-4/M82	0.97951	1
1-3/M82	0.92546	N/A
2-1-1/M82	0.85714	0.92
2-1/M82	1.25291	N/A
2-6/M82	1.00355	1
3-2/M82	1.01948	0.717
4-1-1/M82	0.9101	1
4-1/M82	0.86849	0.69
4-3-2/M82	0.75401	N/A
4-3/M82	1.13727	1
5-3/M82	0.95918	1
6-2/M82	0.94644	1
6-3/M82	0.98244	1
7-1/M82	1.06303	1
7-2/M82	0.90822	0.578
9-3-2/M82	0.95351	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86374	0.321
IL2-6/WTpooled	0.99146	1
IL7-5/WTpooled	1.48596	0.792
IL7-3/WTpooled	0.84867	0.418
IL12-4/WTpooled	0.96747	1
IL1-4/WTpooled	1.19559	1
WT/WTpooled	0.95372	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	0.98877	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00813	1
DC3000/delta hrp 6h	1.19386	1
DC3000/delta hrp 12h	0.9423	1
DC3000/delta hrp 24h	0.95761	0.654

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1	1
DC3000 delta B/DC3000 delta AB	1.12271	0.284

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0034	1
Exp 36h	1.24973	0.693
Exp 60h	1.3098	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05181	1
Var 0h	1.2845	0.782
Var 12h I row2-row1	1.06563	0.443
Var 12h NI row2-row1	1.01147	1
Var 36h I row2-row1	1.05173	1
Var 36h NI row2-row1	0.79938	0.45
Var 60h I row2-row1	1.10672	1
Var 60h NI row2-row1	1.18397	0.904
Time course 0hI-0hNI	1.10801	0.323
Time course 12hI-12hNI	1.087	0.567
Time course 36hI-36hNI	1.01859	0.881
Time course 60hI-60hNI	1.37244	0.008

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)	1.05918	0.297
transgenic ySAMdc/azygous control (breaker)	0.83621	0.173
transgenic ySAMdc/azygous control (red)	0.82303	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03693	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02928	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.64639	0.172
Manapal/WT (break)	0.76858	0.333
Manapal/WT (red)	0.5844	0.181