Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.1.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.08002	0.052
27DAP/17DAP	1.31639	0.741
39DAP/27DAP	1.37554	0.507
41DAP/39DAP	0.61476	0.055
42DAP/41DAP	2.29667	0.033
43DAP/42DAP	2.23412	0.279
47DAP/43DAP	2.06979	0.326
52DAP/47DAP	1.56274	0.46
57DAP/52DAP	1.84261	0.941

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72519	0.03
17DAP/reference	0.63893	0.01
27DAP/reference	1.24295	0.034
39DAP/reference	1.23268	0.091
41DAP/reference	0.97981	0.667
42DAP/reference	2.40248	0.001
43DAP/reference	1.37119	0.089
47DAP/reference	2.09147	0.001
52DAP/reference	1.92335	0.011
57DAP/reference	1.41474	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48557	0.064
27DAP/17DAP	1.04959	0.932
39DAP/27DAP	1.14663	0.519
41DAP/39DAP	1.17738	1
42DAP/41DAP	1.75633	0.012
43DAP/42DAP	1.24856	0.162
47DAP/43DAP	1.21023	0.218
52DAP/47DAP	2.0393	0.048
57DAP/52DAP	1.36223	0.32
57DAP/7DAP	3.78899	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9078	0.296
17DAP/reference	0.92244	0.124
27DAP/reference	0.85963	0.082
39DAP/reference	0.92025	0.23
41DAP/reference	0.72605	0.062
42DAP/reference	0.98974	0.582
43DAP/reference	1.16582	0.603
47DAP/reference	2.16302	0.023
52DAP/reference	0.48305	0.012
57DAP/reference	0.61666	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63051	0.006
17DAP/reference	0.68573	0.007
27DAP/reference	1.49252	0.093
39DAP/reference	1.31071	0.077
41DAP/reference	1.39728	0.007
42DAP/reference	1.7177	0.007
43DAP/reference	0.81239	0.125
47DAP/reference	1.38263	0.011
52DAP/reference	0.96057	0.187
57DAP/reference	0.88186	0.169

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67211	0.039
17DAP/reference	0.78869	0.186
27DAP/reference	0.71531	0.053
39DAP/reference	1.21774	0.104
41DAP/reference	0.93041	0.264
42DAP/reference	1.5747	0.013
43DAP/reference	2.3355	0.006
47DAP/reference	2.04814	0.005
52DAP/reference	5.18403	0.027
57DAP/reference	1.74714	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03006	1
26DAP/20DAP	1.1728	0.558
34DAP/26DAP	0.79394
51DAP/34DAP	2.17249	0.032
52DAP/51DAP	0.82208	1
53DAP/52DAP	0.9872	0.902
55DAP/53DAP	1.06347	0.955
57DAP/55DAP	0.95362	0.817
62DAP/57DAP	0.86755
68DAP/62DAP	1.50465	0.298
68DAP/14DAP	1.33029	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	11.0261	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.04959
Mature Green Tomato/Ripe Tomato	0.17745	0.017
Immature Eggplant/Mature Eggplant	3.30429	0.05
Ripe Pepper/Ripe Tomato	0.08571	0.224
Mature Eggplant/Ripe Tomato	0.04276

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	2.93116
12-2/M82	N/A	N/A
12-4/M82	1.86332
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.97754	1
4-1-1/M82	N/A	N/A
4-1/M82	4.19043
4-3-2/M82	1.97519
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.95274
7-2/M82	N/A	N/A
9-3-2/M82	2.1156	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04722	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.471
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.99095
IL1-4/WTpooled	1.44842	1
WT/WTpooled	N/A	N/A

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	1.00277	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.89592	0.95
DC3000/delta hrp 12h	1.02899	1
DC3000/delta hrp 24h	1.13676	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.46545
DC3000 delta B/DC3000 delta AB	0.86309	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04823	1
Exp 36h	1.68833	0.489
Exp 60h	1.08001	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97385	1
Var 0h	1.14003	0.421
Var 12h I row2-row1	1.01318	1
Var 12h NI row2-row1	0.67698	1
Var 36h I row2-row1	1.29643	0.742
Var 36h NI row2-row1	1.18409	1
Var 60h I row2-row1	1.10871
Var 60h NI row2-row1	1.00881	1
Time course 0hI-0hNI	1.06544	0.574
Time course 12hI-12hNI	1.00946	0.892
Time course 36hI-36hNI	1.04402	0.651
Time course 60hI-60hNI	0.95828	0.646

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)	1.30631	0.372
transgenic ySAMdc/azygous control (breaker)	1.46345	1
transgenic ySAMdc/azygous control (red)	1.03283	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.76959	0.028

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.1633	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.26475	0.14
Manapal/WT (break)	1.13316	1
Manapal/WT (red)	1.01696	1