Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.17.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64068	0.221
27DAP/17DAP	1.18677	0.842
39DAP/27DAP	1.82854	0.244
41DAP/39DAP	2.74242	0.464
42DAP/41DAP	0.78558	1
43DAP/42DAP	1.04503	1
47DAP/43DAP	1.16746	0.776
52DAP/47DAP	1.00097	0.942
57DAP/52DAP	1.05945	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22658	0.085
17DAP/reference	0.95874	0.503
27DAP/reference	1.29018	0.057
39DAP/reference	1.3207	0.039
41DAP/reference	1.33947	0.019
42DAP/reference	1.20679	0.338
43DAP/reference	0.99915	0.805
47DAP/reference	1.10583	0.34
52DAP/reference	1.35961	0.024
57DAP/reference	1.2268	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73087	0.251
27DAP/17DAP	1.24065	0.554
39DAP/27DAP	1.21493	0.471
41DAP/39DAP	1.0522	0.914
42DAP/41DAP	0.88528	0.486
43DAP/42DAP	1.23068	0.513
47DAP/43DAP	1.42741	0.221
52DAP/47DAP	1.17574	0.593
57DAP/52DAP	0.88468	0.352
57DAP/7DAP	1.20218	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79734	0.146
17DAP/reference	0.7503	0.013
27DAP/reference	1.05554	0.664
39DAP/reference	0.7339	0.013
41DAP/reference	0.77181	0.056
42DAP/reference	0.87502	0.16
43DAP/reference	0.75969	0.011
47DAP/reference	1.00894	0.671
52DAP/reference	0.79599	0.013
57DAP/reference	0.78478	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13396	0.832
17DAP/reference	1.32451	0.023
27DAP/reference	1.37306	0.068
39DAP/reference	1.40387	0.043
41DAP/reference	1.4411	0.029
42DAP/reference	1.58584	0.05
43DAP/reference	1.5793	0.021
47DAP/reference	1.32896	0.009
52DAP/reference	1.2215	0.069
57DAP/reference	1.04238	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78513	0.049
17DAP/reference	0.90653	0.389
27DAP/reference	0.70362	0.031
39DAP/reference	0.86609	0.092
41DAP/reference	0.93056	0.264
42DAP/reference	1.0787	0.45
43DAP/reference	0.80803	0.116
47DAP/reference	1.02971	0.687
52DAP/reference	0.96303	0.611
57DAP/reference	1.21003	0.592

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94788	1
26DAP/20DAP	0.82631	0.512
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.79485	0.537
52DAP/51DAP	1.01109	1
53DAP/52DAP	1.2806	0.688
55DAP/53DAP	1.18706	0.834
57DAP/55DAP	0.85297	0.575
62DAP/57DAP	0.82589	0.466
68DAP/62DAP	1.19494	0.971
68DAP/14DAP	1.30369

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79018	0.198

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	N/A	N/A
Mature Eggplant/Ripe Tomato	1.11889

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09998	0.574
1-1-2/M82	1.16206
12-2/M82	N/A	N/A
12-4/M82	1.35138	0.611
1-3/M82	0.57811
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.89384	1
3-2/M82	0.73258
4-1-1/M82	1.21176
4-1/M82	1.46493
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96552	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	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88986	0.321
IL2-6/WTpooled	1.14861	0.584
IL7-5/WTpooled	1.15361	0.792
IL7-3/WTpooled	1.04024	1
IL12-4/WTpooled	0.94081	1
IL1-4/WTpooled	1.35125	1
WT/WTpooled	1.03523	0.999

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	0.97247	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06441	0.671
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.76626
DC3000/delta hrp 24h	1.1779	0.129

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	0.27527

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	0.98949	1
Var 0h	1.07931	0.98
Var 12h I row2-row1	1.04709	1
Var 12h NI row2-row1	0.80263	0.713
Var 36h I row2-row1	0.97583	0.313
Var 36h NI row2-row1	0.91917	0.743
Var 60h I row2-row1	0.83576	0.285
Var 60h NI row2-row1	1.02368	1
Time course 0hI-0hNI	0.97925	0.886
Time course 12hI-12hNI	0.99933	1
Time course 36hI-36hNI	0.94085	0.344
Time course 60hI-60hNI	1.07989	0.254

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.07428	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	1.04358	1

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)	1.21635	0.381
Manapal/WT (red)	0.75311	0.181