Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.7.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96012	0.722
27DAP/17DAP	0.86903	0.641
39DAP/27DAP	1.81964	0.074
41DAP/39DAP	0.53101	0.042
42DAP/41DAP	1.00972	1
43DAP/42DAP	0.8449	0.705
47DAP/43DAP	0.86054	0.555
52DAP/47DAP	0.8653	0.618
57DAP/52DAP	1.32389	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57803	0.019
17DAP/reference	1.25694	0.104
27DAP/reference	1.14512	0.285
39DAP/reference	1.23584	0.286
41DAP/reference	1.00484	0.814
42DAP/reference	1.58643	0.001
43DAP/reference	1.21441	0.042
47DAP/reference	1.09162	0.101
52DAP/reference	1.07916	0.576
57DAP/reference	1.30924	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26904	0.127
27DAP/17DAP	0.9861	0.821
39DAP/27DAP	0.89251	0.201
41DAP/39DAP	1.16888	0.469
42DAP/41DAP	1.02351	1
43DAP/42DAP	0.84463	0.025
47DAP/43DAP	1.06978	0.735
52DAP/47DAP	0.83999	0.18
57DAP/52DAP	0.94762	0.66
57DAP/7DAP	0.64967	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49934	0.026
17DAP/reference	1.70463	0.006
27DAP/reference	2.1116	0.006
39DAP/reference	1.85681	0.005
41DAP/reference	1.66624	0.008
42DAP/reference	1.77858	0.012
43DAP/reference	1.53099	0.014
47DAP/reference	1.25866	0.023
52DAP/reference	2.15491	0.007
57DAP/reference	1.76274	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98578	0.756
17DAP/reference	1.42847	0.061
27DAP/reference	1.7815	0.029
39DAP/reference	1.56319	0.016
41DAP/reference	1.61311	0.008
42DAP/reference	1.74626	0.007
43DAP/reference	0.98328	0.516
47DAP/reference	1.5703	0.008
52DAP/reference	0.96527	0.28
57DAP/reference	0.946	0.408

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39148	0.021
17DAP/reference	1.23203	0.311
27DAP/reference	1.5317	0.02
39DAP/reference	1.76361	0.007
41DAP/reference	1.69038	0.006
42DAP/reference	1.61265	0.007
43DAP/reference	1.79594	0.024
47DAP/reference	0.94601	0.383
52DAP/reference	1.20275	0.412
57DAP/reference	2.0476	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05264	1
26DAP/20DAP	1.60986	0.399
34DAP/26DAP	1.1415	1
51DAP/34DAP	0.81941	0.098
52DAP/51DAP	0.69407	0.151
53DAP/52DAP	0.79087	0.177
55DAP/53DAP	1.0642	0.807
57DAP/55DAP	0.8355	0.391
62DAP/57DAP	1.21061	0.393
68DAP/62DAP	1.658	0.035
68DAP/14DAP	1.96103	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20054	0.14

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.18865	0.075
Mature Green Tomato/Ripe Tomato	1.5977	0.086
Immature Eggplant/Mature Eggplant	0.90279	0.159
Ripe Pepper/Ripe Tomato	0.90112	1
Mature Eggplant/Ripe Tomato	2.37245	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87249	0.907
1-1-2/M82	1.37208	1
12-2/M82	0.94103	0.862
12-4/M82	1.24237	1
1-3/M82	1.48082	0.26
2-1-1/M82	0.93733	1
2-1/M82	0.85353	1
2-6/M82	0.992	1
3-2/M82	1.01822	0.84
4-1-1/M82	1.26399	0.977
4-1/M82	1.90542	0.512
4-3-2/M82	1.70814	0.241
4-3/M82	1.21278	1
5-3/M82	1.11758	1
6-2/M82	0.94589
6-3/M82	0.9909	1
7-1/M82	1.01633	1
7-2/M82	1.12646	1
9-3-2/M82	1.21464	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.61751	0.243
IL2-6/WTpooled	1.29408	0.788
IL7-5/WTpooled	0.87247	1
IL7-3/WTpooled	0.65558	0.31
IL12-4/WTpooled	0.77007	0.71
IL1-4/WTpooled	0.8038	0.457
WT/WTpooled	1.00576	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	1.18799	0.148

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02319	1
DC3000/delta hrp 6h	0.90333	0.95
DC3000/delta hrp 12h	1.10288	1
DC3000/delta hrp 24h	0.93055	0.598

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26505	0.29
DC3000 delta B/DC3000 delta AB	1.1702	0.472

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	0.99499	1
Var 0h	4.3941	0.936
Var 12h I row2-row1	1.0488	0.736
Var 12h NI row2-row1	1.01502	1
Var 36h I row2-row1	1.3141	0.601
Var 36h NI row2-row1	0.85446	0.549
Var 60h I row2-row1	1.02404	1
Var 60h NI row2-row1	0.82252	0.292
Time course 0hI-0hNI	0.89587	0.213
Time course 12hI-12hNI	1.0601	0.55
Time course 36hI-36hNI	1.12412	0.58
Time course 60hI-60hNI	1.08459	0.673

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)	0.97963	0.789
transgenic ySAMdc/azygous control (breaker)	1.03832	1
transgenic ySAMdc/azygous control (red)	1.10139	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.1974	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84517	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77959	0.172
Manapal/WT (break)	0.98761	1
Manapal/WT (red)	1.69694	0.133