Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.2.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	9.34929	0.018
27DAP/17DAP	1.53021	0.636
39DAP/27DAP	1.82671	0.072
41DAP/39DAP	0.62419	0.068
42DAP/41DAP	1.85738	0.722
43DAP/42DAP	1.59176	0.778
47DAP/43DAP	1.15578	0.733
52DAP/47DAP	0.59816	0.169
57DAP/52DAP	2.67586	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.51314	0.027
17DAP/reference	1.13183	0.442
27DAP/reference	2.79863	0.007
39DAP/reference	1.98366	0.053
41DAP/reference	1.79027	0.014
42DAP/reference	3.3238	0.001
43DAP/reference	3.61339	0.006
47DAP/reference	4.61754	0.001
52DAP/reference	2.52673	0.014
57DAP/reference	2.01402	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.19712	0.036
27DAP/17DAP	1.55019	0.754
39DAP/27DAP	0.67056
41DAP/39DAP	1.87028	0.753
42DAP/41DAP	1.06822	0.759
43DAP/42DAP	1.16499	0.83
47DAP/43DAP	1.34302	0.678
52DAP/47DAP	1.42895	0.73
57DAP/52DAP	0.8393	0.39
57DAP/7DAP	3.78508	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93029	0.445
17DAP/reference	1.56759	0.006
27DAP/reference	1.47655	0.03
39DAP/reference	2.34732	0.005
41DAP/reference	2.39163	0.008
42DAP/reference	3.92789	0.006
43DAP/reference	4.10083	0.006
47DAP/reference	4.38476	0.014
52DAP/reference	4.57138	0.007
57DAP/reference	3.55275	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.42177	0.011
17DAP/reference	2.29848	0.016
27DAP/reference	2.99566	0.013
39DAP/reference	2.59559	0.014
41DAP/reference	4.61089	0.005
42DAP/reference	3.63771	0.007
43DAP/reference	1.43495	0.89
47DAP/reference	2.38239	0.01
52DAP/reference	2.30786	0.006
57DAP/reference	1.20204	0.848

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.20143	0.023
17DAP/reference	1.52717	0.665
27DAP/reference	0.98629	0.727
39DAP/reference	2.24483	0.015
41DAP/reference	1.14704	0.674
42DAP/reference	3.8769	0.012
43DAP/reference	5.51173	0.015
47DAP/reference	4.39497	0.005
52DAP/reference	2.97233	0.027
57DAP/reference	6.75562	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.58867	0.966
26DAP/20DAP	1.08297	0.931
34DAP/26DAP	0.66938	0.091
51DAP/34DAP	0.46395	0.054
52DAP/51DAP	0.75054	0.151
53DAP/52DAP	2.44895	0.032
55DAP/53DAP	0.58464	0.024
57DAP/55DAP	0.95183	0.76
62DAP/57DAP	0.67013	0.01
68DAP/62DAP	1.4807	0.039
68DAP/14DAP	0.80065	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.75989	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40029	0.058
Mature Green Tomato/Ripe Tomato	1.0782	0.948
Immature Eggplant/Mature Eggplant	0.78831	0.092
Ripe Pepper/Ripe Tomato	0.665	0.224
Mature Eggplant/Ripe Tomato	0.58996	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.37168	0.477
1-1-2/M82	1.34896	1
12-2/M82	1.11506	1
12-4/M82	0.80611	1
1-3/M82	1.09131	1
2-1-1/M82	0.85692	0.92
2-1/M82	0.52071	0.519
2-6/M82	0.77431	1
3-2/M82	0.34879	0.214
4-1-1/M82	0.75188	1
4-1/M82	0.77899
4-3-2/M82	0.8274	1
4-3/M82	0.80214	0.72
5-3/M82	1.06181	1
6-2/M82	0.55925	1
6-3/M82	1.16417	1
7-1/M82	1.15134	0.539
7-2/M82	0.69047	0.444
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.09429
IL7-3/WTpooled	1.00626	1
IL12-4/WTpooled	0.94268	1
IL1-4/WTpooled	1.08526	1
WT/WTpooled	1.04616	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	0.88926	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03437	0.921
DC3000/delta hrp 6h	0.89659	0.95
DC3000/delta hrp 12h	1.22919	1
DC3000/delta hrp 24h	0.5376	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93067
DC3000 delta B/DC3000 delta AB	1.104	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86902	1
Exp 36h	0.96066	0.943
Exp 60h	0.94926	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00643	1
Var 0h	0.68768	1
Var 12h I row2-row1	0.73889	0.353
Var 12h NI row2-row1	1.05316	1
Var 36h I row2-row1	0.9413	1
Var 36h NI row2-row1	1.04144	1
Var 60h I row2-row1	0.92608	0.952
Var 60h NI row2-row1	0.79997	0.69
Time course 0hI-0hNI	0.99601	1
Time course 12hI-12hNI	0.92303	0.377
Time course 36hI-36hNI	1.03762	0.975
Time course 60hI-60hNI	1.70357	0.009

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)	1.05968	0.541
transgenic ySAMdc/azygous control (breaker)	0.58604	0.139
transgenic ySAMdc/azygous control (red)	0.79206	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.47101	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61929	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06457	1
Manapal/WT (break)	0.78923	1
Manapal/WT (red)	1.66054	0.222