Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.7.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96172	0.728
27DAP/17DAP	0.9736	0.978
39DAP/27DAP	1.45714	0.307
41DAP/39DAP	0.86398	0.483
42DAP/41DAP	1.17881	0.852
43DAP/42DAP	1.06907	0.968
47DAP/43DAP	1.06013	0.793
52DAP/47DAP	0.95042	0.837
57DAP/52DAP	0.94137	0.81

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96178	0.465
17DAP/reference	0.86728	0.298
27DAP/reference	0.78446	0.073
39DAP/reference	0.83376	0.213
41DAP/reference	0.69559	0.114
42DAP/reference	1.22474	0.043
43DAP/reference	0.97503	0.708
47DAP/reference	1.197	0.005
52DAP/reference	1.24531	0.022
57DAP/reference	1.19046	0.052

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18472	0.065
27DAP/17DAP	0.92197	0.684
39DAP/27DAP	0.95999	0.747
41DAP/39DAP	1.1248	0.861
42DAP/41DAP	1.05593	0.872
43DAP/42DAP	0.86151	0.028
47DAP/43DAP	1.02718	0.873
52DAP/47DAP	1.01113	0.979
57DAP/52DAP	1.00368	0.897
57DAP/7DAP	1.02521	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53614	0.076
17DAP/reference	0.54912	0.011
27DAP/reference	0.54054	0.01
39DAP/reference	0.50059	0.011
41DAP/reference	0.67499	0.056
42DAP/reference	0.58684	0.01
43DAP/reference	0.43018	0.01
47DAP/reference	0.88716	0.383
52DAP/reference	0.47627	0.011
57DAP/reference	0.37712	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64638	0.067
17DAP/reference	0.94533	0.357
27DAP/reference	1.48293	0.039
39DAP/reference	1.41946	0.106
41DAP/reference	1.46289	0.062
42DAP/reference	1.33153	0.118
43DAP/reference	0.66419	0.054
47DAP/reference	1.02121	0.66
52DAP/reference	0.98122	0.5
57DAP/reference	0.68297	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.49902	0.028
17DAP/reference	0.81778	0.243
27DAP/reference	0.53659	0.03
39DAP/reference	0.58859	0.015
41DAP/reference	0.66487	0.055
42DAP/reference	1.04929	0.671
43DAP/reference	1.65335	0.565
47DAP/reference	1.17866	0.543
52DAP/reference	0.71341	0.122
57DAP/reference	2.32536	0.031

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2214	0.966
26DAP/20DAP	1.05542	0.793
34DAP/26DAP	1.21671	0.19
51DAP/34DAP	1.03587	0.785
52DAP/51DAP	1.14205	0.123
53DAP/52DAP	0.9332	0.807
55DAP/53DAP	1.04509	0.781
57DAP/55DAP	0.85604	0.433
62DAP/57DAP	1.1741	0.35
68DAP/62DAP	1.78393	0.088
68DAP/14DAP	2.16558	0.077

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27689	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76614	0.226
Mature Green Tomato/Ripe Tomato	1.06591	0.881
Immature Eggplant/Mature Eggplant	1.29187	0.058
Ripe Pepper/Ripe Tomato	0.88884	1
Mature Eggplant/Ripe Tomato	1.32597	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.86589	0.934
1-1-2/M82	1.14281	1
12-2/M82	0.91023	0.727
12-4/M82	1.10057	1
1-3/M82	2.54878	0.277
2-1-1/M82	1.06119	1
2-1/M82	0.87389	0.74
2-6/M82	1.00863	1
3-2/M82	1.0662	0.463
4-1-1/M82	1.1705	1
4-1/M82	1.23758	1
4-3-2/M82	1.19922	1
4-3/M82	1.24566	1
5-3/M82	1.25177	0.572
6-2/M82	1.20419	1
6-3/M82	1.08254	1
7-1/M82	0.98054	1
7-2/M82	1.1837	1
9-3-2/M82	1.07361	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.37274	0.584
IL7-5/WTpooled	0.43175
IL7-3/WTpooled	0.90016	1
IL12-4/WTpooled	0.93835	1
IL1-4/WTpooled	0.9015	0.834
WT/WTpooled	0.9433	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	1.46902	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08017
DC3000/delta hrp 6h	1.02247	1
DC3000/delta hrp 12h	1.41245	1
DC3000/delta hrp 24h	1.20561	0.123

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07826	0.476
DC3000 delta B/DC3000 delta AB	1.17386	0.243

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	1.0104	1
Var 0h	1.18362	0.594
Var 12h I row2-row1	1.01929	1
Var 12h NI row2-row1	1.01427	1
Var 36h I row2-row1	1.187	0.298
Var 36h NI row2-row1	1.03715	1
Var 60h I row2-row1	0.88807	0.832
Var 60h NI row2-row1	0.95612	1
Time course 0hI-0hNI	0.91368	0.269
Time course 12hI-12hNI	1.04998	0.682
Time course 36hI-36hNI	1.10981	0.023
Time course 60hI-60hNI	0.7675	0.011

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)	0.9875	0.789
transgenic ySAMdc/azygous control (breaker)	1.20577	0.248
transgenic ySAMdc/azygous control (red)	1.18894	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12345	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81772	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84698	1
Manapal/WT (break)	0.94127	1
Manapal/WT (red)	1.40476	0.137