Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.17.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.67161	0.052
27DAP/17DAP	1.19349	0.89
39DAP/27DAP	1.0763	1
41DAP/39DAP	1.02004	0.967
42DAP/41DAP	1.204	0.696
43DAP/42DAP	1.4473	0.47
47DAP/43DAP	1.57012	0.469
52DAP/47DAP	1.05374	0.845
57DAP/52DAP	0.93127	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99453	0.707
17DAP/reference	0.81887	0.018
27DAP/reference	0.91001	0.265
39DAP/reference	0.89885	0.284
41DAP/reference	0.81021	0.154
42DAP/reference	1.06846	0.842
43DAP/reference	1.02937	0.73
47DAP/reference	1.17534	0.023
52DAP/reference	1.16396	0.524
57DAP/reference	1.00522	0.701

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03417	0.91
27DAP/17DAP	1.04313	0.9
39DAP/27DAP	0.97437	0.887
41DAP/39DAP	0.92925	0.822
42DAP/41DAP	1.14656	0.308
43DAP/42DAP	1.53163	0.134
47DAP/43DAP	1.01487	0.963
52DAP/47DAP	0.92109	0.671
57DAP/52DAP	1.24263	0.424
57DAP/7DAP	1.11798	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17529	0.129
17DAP/reference	0.70125	0.056
27DAP/reference	0.97866	0.494
39DAP/reference	0.9193	0.264
41DAP/reference	1.2249	0.416
42DAP/reference	0.80322	0.063
43DAP/reference	0.97592	0.48
47DAP/reference	1.00417	1
52DAP/reference	0.70838	0.15
57DAP/reference	0.90399	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42447	0.589
17DAP/reference	1.004	0.805
27DAP/reference	1.05422	0.974
39DAP/reference	1.17471	0.136
41DAP/reference	1.10137	0.513
42DAP/reference	1.07784	0.509
43DAP/reference	0.94511	0.438
47DAP/reference	0.92342	0.168
52DAP/reference	0.92009	0.302
57DAP/reference	0.70992	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.963	0.526
17DAP/reference	0.96984	0.636
27DAP/reference	0.85742	0.108
39DAP/reference	0.93197	0.246
41DAP/reference	1.05852	0.714
42DAP/reference	1.02834	0.943
43DAP/reference	1.29907	0.041
47DAP/reference	1.27165	0.022
52DAP/reference	1.86593	0.093
57DAP/reference	1.35982	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01771	1
26DAP/20DAP	1.31222
34DAP/26DAP	1.31976	1
51DAP/34DAP	1.47099	0.251
52DAP/51DAP	1.71979
53DAP/52DAP	0.97087	0.868
55DAP/53DAP	0.91797	0.592
57DAP/55DAP	1.38969	0.376
62DAP/57DAP	1.08099	1
68DAP/62DAP	1.29662	0.872
68DAP/14DAP	1.26842	0.739

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30331	0.347

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	13.4374	0.69
Immature Eggplant/Mature Eggplant	1.42972	0.055
Ripe Pepper/Ripe Tomato	0.27829	0.224
Mature Eggplant/Ripe Tomato	0.60514	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86336
1-1-2/M82	1.05324	1
12-2/M82	0.81753	0.639
12-4/M82	0.85804	0.358
1-3/M82	N/A	N/A
2-1-1/M82	1.66092
2-1/M82	0.72507
2-6/M82	1.36449
3-2/M82	1.50683	0.717
4-1-1/M82	1.07272
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.19009	1
5-3/M82	1.13259	1
6-2/M82	N/A	N/A
6-3/M82	0.8087	0.375
7-1/M82	1.26908
7-2/M82	N/A	N/A
9-3-2/M82	1.13373	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87782
IL2-6/WTpooled	0.76313	0.473
IL7-5/WTpooled	1.73381
IL7-3/WTpooled	0.82726
IL12-4/WTpooled	0.93785	0.71
IL1-4/WTpooled	0.97077	0.415
WT/WTpooled	1.164	0.777

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	0.84517	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97792	1
DC3000/delta hrp 6h	0.92527	0.95
DC3000/delta hrp 12h	0.72162	1
DC3000/delta hrp 24h	1.00782	0.821

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	N/A	N/A
Exp 36h	0.75426	0.449
Exp 60h	1.18559	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9828	1
Var 0h	0.53923	0.98
Var 12h I row2-row1	1.12149	0.795
Var 12h NI row2-row1	1.13859	1
Var 36h I row2-row1	1.24676	0.298
Var 36h NI row2-row1	0.56026	0.522
Var 60h I row2-row1	1.30685	0.543
Var 60h NI row2-row1	0.95705	1
Time course 0hI-0hNI	0.91717	0.519
Time course 12hI-12hNI	1.04385	0.663
Time course 36hI-36hNI	1.21875	0.248
Time course 60hI-60hNI	1.1719	0.06

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)	0.96599	0.614
transgenic ySAMdc/azygous control (breaker)	0.88875	0.49
transgenic ySAMdc/azygous control (red)	1.07063	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87817	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9973	1
Manapal/WT (break)	1.1632	0.381
Manapal/WT (red)	1.24303	0.413