Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.5.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84439	0.475
27DAP/17DAP	0.78934	0.539
39DAP/27DAP	0.81871	0.487
41DAP/39DAP	0.88923	0.636
42DAP/41DAP	1.21991	0.488
43DAP/42DAP	1.40523	0.346
47DAP/43DAP	1.2594	0.647
52DAP/47DAP	1.07763	0.843
57DAP/52DAP	0.8234	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94117	0.422
17DAP/reference	0.9502	0.474
27DAP/reference	0.85101	0.182
39DAP/reference	1.00943	1
41DAP/reference	0.92361	0.341
42DAP/reference	0.90402	0.069
43DAP/reference	1.07249	0.596
47DAP/reference	0.97151	0.418
52DAP/reference	0.91426	0.172
57DAP/reference	1.02184	0.805

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71974	0.135
27DAP/17DAP	0.87368	0.724
39DAP/27DAP	1.01505	1
41DAP/39DAP	0.85311	0.662
42DAP/41DAP	1.04345	0.872
43DAP/42DAP	1.1524	0.192
47DAP/43DAP	1.47155	0.114
52DAP/47DAP	1.03772	0.969
57DAP/52DAP	0.68238	0.116
57DAP/7DAP	1.16439	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00673	1
17DAP/reference	0.97591	0.447
27DAP/reference	1.03931	0.974
39DAP/reference	0.80368	0.031
41DAP/reference	1.05065	0.791
42DAP/reference	1.24055	0.132
43DAP/reference	0.99351	0.637
47DAP/reference	0.96835	0.671
52DAP/reference	0.94098	0.179
57DAP/reference	0.86116	0.045

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18692	0.477
17DAP/reference	0.9082	0.307
27DAP/reference	0.9698	0.554
39DAP/reference	0.9202	0.33
41DAP/reference	0.98287	0.459
42DAP/reference	0.83328	0.073
43DAP/reference	1.40314	0.086
47DAP/reference	0.90807	0.188
52DAP/reference	0.906	0.239
57DAP/reference	0.98639	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00113	1
17DAP/reference	1.01018	0.9
27DAP/reference	0.95594	0.397
39DAP/reference	1.16256	0.062
41DAP/reference	0.85565	0.086
42DAP/reference	1.01923	1
43DAP/reference	1.03295	0.867
47DAP/reference	1.06842	0.901
52DAP/reference	0.81025	0.174
57DAP/reference	0.86329	0.152

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04872	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	0.47857
51DAP/34DAP	1.29988	0.314
52DAP/51DAP	1.01365	0.954
53DAP/52DAP	0.91417	0.741
55DAP/53DAP	1.2751	0.982
57DAP/55DAP	0.72343	0.184
62DAP/57DAP	1.04153	0.868
68DAP/62DAP	0.89594	0.722
68DAP/14DAP	2.19755	0.065

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03407	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.02114	1
Mature Eggplant/Ripe Tomato	0.49054	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.24264
12-2/M82	1.20913	0.61
12-4/M82	0.95748
1-3/M82	1.25566	1
2-1-1/M82	0.89789	0.92
2-1/M82	N/A	N/A
2-6/M82	1.10879	0.505
3-2/M82	N/A	N/A
4-1-1/M82	0.90538	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.46401	0.268
5-3/M82	0.76007	0.642
6-2/M82	1.22715
6-3/M82	1.10871	1
7-1/M82	0.81066
7-2/M82	1.38212
9-3-2/M82	2.02927

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17143	0.493
IL2-6/WTpooled	1.09318	0.788
IL7-5/WTpooled	0.85808	0.559
IL7-3/WTpooled	1.14657	1
IL12-4/WTpooled	0.88444	0.543
IL1-4/WTpooled	1.02917	1
WT/WTpooled	0.87802	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	0.62452

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0579	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.19814	1
DC3000/delta hrp 24h	0.72914	0.034

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	2.64045

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0645	1
Var 0h	1.16675	0.936
Var 12h I row2-row1	1.10912	0.654
Var 12h NI row2-row1	1.02129	1
Var 36h I row2-row1	1.35204
Var 36h NI row2-row1	0.87821	0.382
Var 60h I row2-row1	1.03452	1
Var 60h NI row2-row1	0.78222	1
Time course 0hI-0hNI	1.04823	0.537
Time course 12hI-12hNI	0.95121	0.738
Time course 36hI-36hNI	1.01901	0.874
Time course 60hI-60hNI	2.00092	0.013

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)	0.92886	0.662
transgenic ySAMdc/azygous control (breaker)	1.40004	0.162
transgenic ySAMdc/azygous control (red)	0.97942	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94901	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31617	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.74892	0.236
Manapal/WT (red)	0.73122	0.188