Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.13.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72447	0.303
27DAP/17DAP	1.05046	1
39DAP/27DAP	0.79	0.402
41DAP/39DAP	0.84808	0.447
42DAP/41DAP	1.00932	1
43DAP/42DAP	0.76431	0.554
47DAP/43DAP	1.15558	0.609
52DAP/47DAP	2.47995	0.327
57DAP/52DAP	0.96277	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00696	1
17DAP/reference	1.10029	0.08
27DAP/reference	1.07923	0.121
39DAP/reference	0.95565	0.381
41DAP/reference	1.01041	1
42DAP/reference	0.86334	0.004
43DAP/reference	0.96109	0.464
47DAP/reference	0.91397	0.007
52DAP/reference	0.95114	0.393
57DAP/reference	1.02373	0.984

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94721	0.526
27DAP/17DAP	1.11337	0.671
39DAP/27DAP	1.35627	0.378
41DAP/39DAP	0.99095	1
42DAP/41DAP	1.13088	0.675
43DAP/42DAP	0.96923	0.729
47DAP/43DAP	0.90594	0.577
52DAP/47DAP	1.04721	0.856
57DAP/52DAP	1.01956	0.926
57DAP/7DAP	1.79058	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81953	0.082
17DAP/reference	0.86714	0.012
27DAP/reference	0.93575	0.171
39DAP/reference	1.01511	1
41DAP/reference	0.86017	0.111
42DAP/reference	0.91447	0.248
43DAP/reference	0.93537	0.321
47DAP/reference	0.92021	0.222
52DAP/reference	0.86107	0.03
57DAP/reference	0.94168	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15525	0.12
17DAP/reference	0.91588	0.317
27DAP/reference	0.9156	0.327
39DAP/reference	0.98138	0.509
41DAP/reference	0.89559	0.061
42DAP/reference	0.8639	0.021
43DAP/reference	1.19255	0.239
47DAP/reference	0.94375	0.292
52DAP/reference	0.95331	0.38
57DAP/reference	0.90288	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02877	0.809
17DAP/reference	1.07593	0.522
27DAP/reference	0.96356	0.206
39DAP/reference	1.012	0.819
41DAP/reference	0.98166	0.618
42DAP/reference	0.82274	0.049
43DAP/reference	0.82478	0.021
47DAP/reference	1.01723	1
52DAP/reference	0.9133	0.415
57DAP/reference	0.92591	0.273

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02211	0.966
26DAP/20DAP	1.1371	0.562
34DAP/26DAP	0.844	0.682
51DAP/34DAP	0.889	0.522
52DAP/51DAP	0.86315	1
53DAP/52DAP	1.204	0.284
55DAP/53DAP	1.10704	0.681
57DAP/55DAP	1.09782	0.915
62DAP/57DAP	1.04915	0.868
68DAP/62DAP	1.12323	0.253
68DAP/14DAP	0.98401	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2648	0.527

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.15887	0.948
Immature Eggplant/Mature Eggplant	1.58567	0.05
Ripe Pepper/Ripe Tomato	0.86821	0.224
Mature Eggplant/Ripe Tomato	1.42005	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05329	1
1-1-2/M82	1.07485	1
12-2/M82	1.22544	0.296
12-4/M82	1.07297
1-3/M82	0.95164	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89904	1
3-2/M82	0.84699	0.752
4-1-1/M82	0.91818	1
4-1/M82	1.8499
4-3-2/M82	1.00266
4-3/M82	0.89843	0.72
5-3/M82	1.11282	1
6-2/M82	0.6663
6-3/M82	0.95642	1
7-1/M82	0.87847
7-2/M82	0.77904
9-3-2/M82	0.82235	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.9389	1
IL7-5/WTpooled	0.60466
IL7-3/WTpooled	0.89019	1
IL12-4/WTpooled	1.00306	1
IL1-4/WTpooled	0.86943
WT/WTpooled	1.01123	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	0.98351	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97055	1
DC3000/delta hrp 6h	1.0299
DC3000/delta hrp 12h	1.02831	1
DC3000/delta hrp 24h	1.07841	0.502

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	0.70948	0.228
Exp 36h	0.95319	0.82
Exp 60h	1.19396	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94183	1
Var 0h	1.11686	1
Var 12h I row2-row1	1.13158	0.296
Var 12h NI row2-row1	0.95045	0.906
Var 36h I row2-row1	0.98724	1
Var 36h NI row2-row1	0.97028	0.478
Var 60h I row2-row1	0.96248	0.952
Var 60h NI row2-row1	1.06361	1
Time course 0hI-0hNI	1.06293	0.764
Time course 12hI-12hNI	1.07108	0.517
Time course 36hI-36hNI	0.92541	0.344
Time course 60hI-60hNI	1.38688	0.011

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)	0.9792	0.789
transgenic ySAMdc/azygous control (breaker)	1.31713	0.178
transgenic ySAMdc/azygous control (red)	1.14902	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99958	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23363	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8855	1
Manapal/WT (break)	0.93187	1
Manapal/WT (red)	0.87405	0.274