Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.16.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.30755	0.264
27DAP/17DAP	0.59111	0.083
39DAP/27DAP	0.65098	0.326
41DAP/39DAP	0.73059	0.171
42DAP/41DAP	0.62299	0.397
43DAP/42DAP	1.28387	0.362
47DAP/43DAP	0.46988	0.053
52DAP/47DAP	0.72475	0.429
57DAP/52DAP	1.22716	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05413	0.544
17DAP/reference	0.97283	0.664
27DAP/reference	0.84365	0.057
39DAP/reference	0.80175	0.1
41DAP/reference	0.75989	0.031
42DAP/reference	0.7545	0.001
43DAP/reference	0.79678	0.031
47DAP/reference	0.64897	0.001
52DAP/reference	0.54737	0.013
57DAP/reference	0.68758	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.68584	0.041
27DAP/17DAP	0.78517	0.218
39DAP/27DAP	0.33702	0.028
41DAP/39DAP	1.40163	0.135
42DAP/41DAP	0.79232	0.048
43DAP/42DAP	0.39854	0.022
47DAP/43DAP	0.76179	0.02
52DAP/47DAP	0.81179	0.226
57DAP/52DAP	0.981	0.776
57DAP/7DAP	0.25802	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70657	0.028
17DAP/reference	1.11248	0.123
27DAP/reference	0.76862	0.019
39DAP/reference	0.65871	0.025
41DAP/reference	0.55497	0.012
42DAP/reference	0.45858	0.01
43DAP/reference	0.50075	0.011
47DAP/reference	0.48878	0.03
52DAP/reference	0.62252	0.019
57DAP/reference	0.71167	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98302	0.756
17DAP/reference	0.95609	0.434
27DAP/reference	1.01528	1
39DAP/reference	0.66595	0.009
41DAP/reference	0.76786	0.011
42DAP/reference	0.78356	0.019
43DAP/reference	0.40392	0.005
47DAP/reference	0.73936	0.01
52DAP/reference	0.57181	0.003
57DAP/reference	0.5248	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.33637	0.015
17DAP/reference	2.77958	0.017
27DAP/reference	2.33675	0.016
39DAP/reference	1.74416	0.006
41DAP/reference	1.2619	0.1
42DAP/reference	0.83947	0.172
43DAP/reference	0.90638	0.246
47DAP/reference	0.72779	0.01
52DAP/reference	0.49846	0.047
57DAP/reference	1.44218	0.049

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.49798	0.752
26DAP/20DAP	0.89531	1
34DAP/26DAP	1.0484	1
51DAP/34DAP	0.88647	0.504
52DAP/51DAP	1.18861	0.454
53DAP/52DAP	0.87473	0.27
55DAP/53DAP	0.84609	0.282
57DAP/55DAP	0.90338	0.532
62DAP/57DAP	0.87425	0.162
68DAP/62DAP	0.96468	0.787
68DAP/14DAP	1.05214	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14862	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.96089	0.058
Mature Green Tomato/Ripe Tomato	7.23542	0.015
Immature Eggplant/Mature Eggplant	0.60961	0.062
Ripe Pepper/Ripe Tomato	0.77441	1
Mature Eggplant/Ripe Tomato	1.92714	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.96346
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15539	0.493
IL2-6/WTpooled	1.23495	0.584
IL7-5/WTpooled	0.76751	1
IL7-3/WTpooled	1.07469	1
IL12-4/WTpooled	1.16027	0.553
IL1-4/WTpooled	1.04986
WT/WTpooled	1.09655	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	1.06002	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94659	1
DC3000/delta hrp 6h	1.00875	1
DC3000/delta hrp 12h	1.3413	1
DC3000/delta hrp 24h	0.69261	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75289
DC3000 delta B/DC3000 delta AB	0.41201	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04118	1
Exp 36h	0.89128	0.449
Exp 60h	0.87475	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01486	1
Var 0h	0.82422	0.933
Var 12h I row2-row1	0.98324	0.856
Var 12h NI row2-row1	0.99685	1
Var 36h I row2-row1	0.92511	0.805
Var 36h NI row2-row1	1.42414	1
Var 60h I row2-row1	1.30726	0.562
Var 60h NI row2-row1	0.96817	0.756
Time course 0hI-0hNI	0.97075	0.702
Time course 12hI-12hNI	1.03007	0.82
Time course 36hI-36hNI	1.10282	0.355
Time course 60hI-60hNI	0.95576	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)	1.21576	0.541
transgenic ySAMdc/azygous control (breaker)	2.81911	0.162
transgenic ySAMdc/azygous control (red)	0.87731	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.72128	0.107

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.60115	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	7.5978	0.083
Manapal/WT (break)	6.58831	0.123
Manapal/WT (red)	2.39302	0.413