Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96709	0.671
27DAP/17DAP	0.57951	0.058
39DAP/27DAP	1.02592	0.857
41DAP/39DAP	0.55208	0.046
42DAP/41DAP	0.80401	0.774
43DAP/42DAP	1.06212	1
47DAP/43DAP	0.64155	0.101
52DAP/47DAP	0.99457	0.907
57DAP/52DAP	1.02691	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70342	0.5
17DAP/reference	1.48717	0.041
27DAP/reference	1.12881	0.863
39DAP/reference	1.44099	0.02
41DAP/reference	1.23759	0.759
42DAP/reference	1.01567	1
43DAP/reference	1.09937
47DAP/reference	1.65506	0.154
52DAP/reference	1.296	0.035
57DAP/reference	2.19329

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4424	0.036
27DAP/17DAP	0.87501	0.446
39DAP/27DAP	0.54545	0.029
41DAP/39DAP	1.2488	0.579
42DAP/41DAP	0.94198	0.572
43DAP/42DAP	0.73595	0.022
47DAP/43DAP	0.93579	0.499
52DAP/47DAP	1.11996	0.639
57DAP/52DAP	1.1108	0.483
57DAP/7DAP	0.5789	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85728	0.27
17DAP/reference	0.58647	0.013
27DAP/reference	0.91993	0.375
39DAP/reference	0.97462	0.474
41DAP/reference	1.13538	1
42DAP/reference	1.08897	0.308
43DAP/reference	0.99614	0.665
47DAP/reference	1.05445	0.915
52DAP/reference	0.87077	0.254
57DAP/reference	0.99433	0.589

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84718	0.17
17DAP/reference	1.05868	0.898
27DAP/reference	1.10167	0.404
39DAP/reference	1.3293	0.324
41DAP/reference	1.09673	0.862
42DAP/reference	1.40054	0.01
43DAP/reference	0.9745	0.62
47DAP/reference	1.21598	0.159
52DAP/reference	1.08759	0.498
57DAP/reference	0.799	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93766	0.489
17DAP/reference	1.08137	0.456
27DAP/reference	1.05046	0.721
39DAP/reference	1.12135	0.027
41DAP/reference	1.30004	0.471
42DAP/reference	1.23087	0.321
43DAP/reference	0.87234	0.197
47DAP/reference	1.05775	0.82
52DAP/reference	0.87752	0.25
57DAP/reference	1.15992	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.5723	0.966
26DAP/20DAP	1.33669	0.196
34DAP/26DAP	1.18539	0.542
51DAP/34DAP	0.77023	0.106
52DAP/51DAP	1.03277	0.77
53DAP/52DAP	0.81568	0.17
55DAP/53DAP	1.12801	0.244
57DAP/55DAP	0.86664	0.468
62DAP/57DAP	0.89282	0.681
68DAP/62DAP	1.54664	0.89
68DAP/14DAP	0.67493	0.035

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.71653	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.43437	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.35178	0.256
Mature Eggplant/Ripe Tomato	1.54114	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90507	0.841
1-1-2/M82	1.08135	1
12-2/M82	N/A	N/A
12-4/M82	1.02432	1
1-3/M82	1.01618
2-1-1/M82	0.90732
2-1/M82	N/A	N/A
2-6/M82	0.77267	0.501
3-2/M82	1.02815	1
4-1-1/M82	0.96403
4-1/M82	N/A	N/A
4-3-2/M82	1.91516
4-3/M82	1.02544	1
5-3/M82	1.12984	1
6-2/M82	1.1463	1
6-3/M82	0.99815	1
7-1/M82	1.26551	0.598
7-2/M82	0.84949	0.553
9-3-2/M82	1.03375	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80081
IL2-6/WTpooled	0.75745	0.383
IL7-5/WTpooled	0.80959	1
IL7-3/WTpooled	0.68557	0.298
IL12-4/WTpooled	1.06386	0.595
IL1-4/WTpooled	0.92287	0.834
WT/WTpooled	0.97872	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	1.02091	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99051	1
DC3000/delta hrp 6h	1.13433
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.231	0.074

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67469	0.025
DC3000 delta B/DC3000 delta AB	0.52166	0.023

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	0.98688	1
Var 0h	21.8902	1
Var 12h I row2-row1	0.90555	0.39
Var 12h NI row2-row1	0.994	1
Var 36h I row2-row1	0.84142	1
Var 36h NI row2-row1	0.97194	0.791
Var 60h I row2-row1	1.0645	0.562
Var 60h NI row2-row1	0.97098	1
Time course 0hI-0hNI	1.01319	1
Time course 12hI-12hNI	1.00553	1
Time course 36hI-36hNI	1.07827	0.128
Time course 60hI-60hNI	0.72605	0.026

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)	1.23989	0.748
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.07571	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.79845	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.19325	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.97696	1
Manapal/WT (red)	0.90083	0.315