Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.3.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07486	0.904
27DAP/17DAP	0.7856	0.483
39DAP/27DAP	1.3363	0.223
41DAP/39DAP	0.6034	0.045
42DAP/41DAP	1.12793	0.937
43DAP/42DAP	1.59182	0.26
47DAP/43DAP	1.32942	0.563
52DAP/47DAP	0.58135	0.057
57DAP/52DAP	1.29571	0.886

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7625	0.06
17DAP/reference	0.63765	0.008
27DAP/reference	0.89449	0.428
39DAP/reference	0.75068	0.027
41DAP/reference	0.55203	0.008
42DAP/reference	0.81013	0.006
43DAP/reference	0.89146	0.098
47DAP/reference	0.97904	0.418
52DAP/reference	1.26045	0.088
57DAP/reference	1.41518	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36029	0.053
27DAP/17DAP	1.18798	0.55
39DAP/27DAP	0.95932	0.768
41DAP/39DAP	0.92702	0.781
42DAP/41DAP	0.86959	0.284
43DAP/42DAP	0.80563	0.101
47DAP/43DAP	1.03337	0.914
52DAP/47DAP	1.37614	0.261
57DAP/52DAP	1.21043	0.378
57DAP/7DAP	0.9829	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38052	0.045
17DAP/reference	1.60931	0.006
27DAP/reference	1.45708	0.014
39DAP/reference	1.76279	0.007
41DAP/reference	1.59307	0.031
42DAP/reference	1.82362	0.007
43DAP/reference	1.53821	0.008
47DAP/reference	1.22084	0.43
52DAP/reference	1.48456	0.012
57DAP/reference	1.77617	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66257	0.009
17DAP/reference	0.61538	0.004
27DAP/reference	0.87804	0.134
39DAP/reference	0.94584	0.281
41DAP/reference	0.95297	0.188
42DAP/reference	0.87461	0.037
43DAP/reference	0.63312	0.011
47DAP/reference	0.73949	0.012
52DAP/reference	0.81324	0.005
57DAP/reference	0.60449	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43883	0.138
17DAP/reference	1.11988	0.924
27DAP/reference	1.51831	0.025
39DAP/reference	1.41826	0.042
41DAP/reference	1.23667	0.031
42DAP/reference	1.39891	0.017
43DAP/reference	1.44031	0.038
47DAP/reference	0.94841	0.383
52DAP/reference	1.28315	0.318
57DAP/reference	1.61853	0.009

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92274	1
26DAP/20DAP	1.54988	0.14
34DAP/26DAP	0.79216	0.192
51DAP/34DAP	1.36754	0.055
52DAP/51DAP	0.78547	0.151
53DAP/52DAP	0.63188	0.049
55DAP/53DAP	0.45651	0.016
57DAP/55DAP	1.00918	0.821
62DAP/57DAP	1.17992	0.569
68DAP/62DAP	2.66282	0.047
68DAP/14DAP	3.22896	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.86737	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.87367	0.401
Mature Green Tomato/Ripe Tomato	1.89651	0.017
Immature Eggplant/Mature Eggplant	0.93164
Ripe Pepper/Ripe Tomato	2.36965	0.258
Mature Eggplant/Ripe Tomato	0.78176	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.67411
1-1-2/M82	0.84971
12-2/M82	N/A	N/A
12-4/M82	1.62511	1
1-3/M82	1.11487
2-1-1/M82	1.03405
2-1/M82	0.91298
2-6/M82	N/A	N/A
3-2/M82	0.76154	1
4-1-1/M82	0.76311
4-1/M82	1.81734
4-3-2/M82	1.3696
4-3/M82	1.1096	1
5-3/M82	1.02199	1
6-2/M82	1.08922	1
6-3/M82	N/A	N/A
7-1/M82	1.05581	1
7-2/M82	N/A	N/A
9-3-2/M82	1.17425	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87542	0.243
IL2-6/WTpooled	1.13377	0.584
IL7-5/WTpooled	0.79571	1
IL7-3/WTpooled	0.96548	1
IL12-4/WTpooled	0.88331	1
IL1-4/WTpooled	1.08649	1
WT/WTpooled	1.00148	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	0.84827	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03855	0.894
DC3000/delta hrp 6h	1.01087	1
DC3000/delta hrp 12h	1.06579	1
DC3000/delta hrp 24h	1.01113	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1017	0.229
DC3000 delta B/DC3000 delta AB	1.23646	0.226

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.69819	1
Exp 36h	0.96868	1
Exp 60h	0.83124	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98416	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.0046	1
Var 12h NI row2-row1	1.10361	0.649
Var 36h I row2-row1	1.18554	0.601
Var 36h NI row2-row1	1.19179	1
Var 60h I row2-row1	0.67811	0.439
Var 60h NI row2-row1	1.08499	1
Time course 0hI-0hNI	1.03306	0.867
Time course 12hI-12hNI	0.8717	0.309
Time course 36hI-36hNI	0.79327	0.03
Time course 60hI-60hNI	0.98112	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)	1.0138	0.541
transgenic ySAMdc/azygous control (breaker)	2.11627	0.166
transgenic ySAMdc/azygous control (red)	1.24023	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08434	0.051

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01129	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16563	0.14
Manapal/WT (break)	1.45758	0.183
Manapal/WT (red)	1.6551	0.133