Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.5.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20476	0.463
27DAP/17DAP	1.39508	0.874
39DAP/27DAP	1.32358	0.752
41DAP/39DAP	0.97477	0.811
42DAP/41DAP	1.26969	0.844
43DAP/42DAP	1.00439	0.937
47DAP/43DAP	1.22073	0.527
52DAP/47DAP	1.39472	0.696
57DAP/52DAP	1.08967	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04644	0.788
17DAP/reference	0.9173	0.194
27DAP/reference	0.95568	0.552
39DAP/reference	0.90072	0.155
41DAP/reference	0.92891	0.434
42DAP/reference	1.08611	0.21
43DAP/reference	1.02951	0.73
47DAP/reference	1.11214	0.478
52DAP/reference	1.17183	0.069
57DAP/reference	0.94326	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83424	0.228
27DAP/17DAP	0.46014
39DAP/27DAP	0.74991	0.334
41DAP/39DAP	1.251	0.656
42DAP/41DAP	1.08913	0.935
43DAP/42DAP	1.01665	1
47DAP/43DAP	1.02708	0.973
52DAP/47DAP	1.14008	0.57
57DAP/52DAP	1.34966	0.363
57DAP/7DAP	1.65516

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02815	1
17DAP/reference	0.96339	0.389
27DAP/reference	1.02853	1
39DAP/reference	1.39872	0.012
41DAP/reference	1.05691	0.836
42DAP/reference	1.64578	0.308
43DAP/reference	0.86583	0.305
47DAP/reference	1.6821	0.404
52DAP/reference	1.06196	0.732
57DAP/reference	0.90871	0.291

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88077	0.342
17DAP/reference	0.907	0.269
27DAP/reference	1.15274	0.23
39DAP/reference	1.01424	0.702
41DAP/reference	0.99238	0.557
42DAP/reference	1.03795	0.81
43DAP/reference	0.97649	0.569
47DAP/reference	0.91999	0.079
52DAP/reference	1.02817	0.938
57DAP/reference	0.8789	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04113	0.758
17DAP/reference	1.32875	0.538
27DAP/reference	0.59496	0.174
39DAP/reference	1.03604	0.912
41DAP/reference	0.9264	0.331
42DAP/reference	0.96531	0.671
43DAP/reference	0.99605	0.738
47DAP/reference	1.33294	0.847
52DAP/reference	0.90706	0.472
57DAP/reference	1.31214	0.04

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.34985	0.966
26DAP/20DAP	1.59761	0.099
34DAP/26DAP	0.68143
51DAP/34DAP	1.12843	0.949
52DAP/51DAP	1.03102	0.873
53DAP/52DAP	1.99788	0.753
55DAP/53DAP	1.1337	0.671
57DAP/55DAP	0.61193	0.243
62DAP/57DAP	1.09777	0.515
68DAP/62DAP	1.32819	0.869
68DAP/14DAP	1.31584	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35881	0.466

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.83029
Mature Green Tomato/Ripe Tomato	0.61217	0.317
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.40169	0.224
Mature Eggplant/Ripe Tomato	0.33478	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06079	1
1-1-2/M82	1.00176
12-2/M82	N/A	N/A
12-4/M82	0.8711	0.272
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	0.57119
2-6/M82	1.0934	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.49316
5-3/M82	1.00143	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.38704
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.92466	0.562
WT/WTpooled	0.8151

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	1.00896	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89658	1
DC3000/delta hrp 6h	1.16172
DC3000/delta hrp 12h	1.06769	1
DC3000/delta hrp 24h	1.02908	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57638	0.024
DC3000 delta B/DC3000 delta AB	0.51295	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11805	1
Exp 36h	1.23989	1
Exp 60h	0.98707	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98756	1
Var 0h	16.1902	0.98
Var 12h I row2-row1	0.91482	0.418
Var 12h NI row2-row1	1.05148	1
Var 36h I row2-row1	1.02629	1
Var 36h NI row2-row1	1.36106	1
Var 60h I row2-row1	0.89708	0.582
Var 60h NI row2-row1	1.05927	1
Time course 0hI-0hNI	0.97392	0.898
Time course 12hI-12hNI	0.97631	0.855
Time course 36hI-36hNI	0.94467	0.366
Time course 60hI-60hNI	0.40266	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)	0.9603	0.454
transgenic ySAMdc/azygous control (breaker)	0.86817	0.15
transgenic ySAMdc/azygous control (red)	0.90075	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97028	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21252	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88719	1
Manapal/WT (break)	1.04309	1
Manapal/WT (red)	1.33009	0.413