Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.3.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97426	0.689
27DAP/17DAP	0.67853	0.359
39DAP/27DAP	0.84095	0.474
41DAP/39DAP	0.86204	0.518
42DAP/41DAP	1.03682	1
43DAP/42DAP	1.21958	0.982
47DAP/43DAP	1.10273	0.84
52DAP/47DAP	1.60614	0.325
57DAP/52DAP	1.0662	0.849

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93557	0.326
17DAP/reference	0.85797	0.043
27DAP/reference	0.91834	0.417
39DAP/reference	0.80417	0.009
41DAP/reference	0.87038	0.201
42DAP/reference	0.92318	0.305
43DAP/reference	1.01601
47DAP/reference	0.79404	0.001
52DAP/reference	0.7756	0.064
57DAP/reference	0.35214

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00926	1
27DAP/17DAP	0.92879	0.648
39DAP/27DAP	0.78405	0.279
41DAP/39DAP	0.92843	0.875
42DAP/41DAP	1.25345	0.291
43DAP/42DAP	1.01423	0.788
47DAP/43DAP	0.8756	0.476
52DAP/47DAP	1.55446	0.366
57DAP/52DAP	1.72396	0.069
57DAP/7DAP	2.25361	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02838	0.758
17DAP/reference	1.23934	0.016
27DAP/reference	1.18274	0.013
39DAP/reference	1.26317	0.059
41DAP/reference	1.17038	0.26
42DAP/reference	1.09535	0.686
43DAP/reference	1.11944	0.511
47DAP/reference	0.96551	0.504
52DAP/reference	1.00242	0.679
57DAP/reference	0.98495	0.549

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98579	0.77
17DAP/reference	0.94017	0.347
27DAP/reference	1.10319	0.437
39DAP/reference	0.95325	0.381
41DAP/reference	0.99859	0.666
42DAP/reference	0.96355	0.355
43DAP/reference	0.81581	0.09
47DAP/reference	0.90354	0.099
52DAP/reference	0.84826	0.034
57DAP/reference	0.91555	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2783	0.074
17DAP/reference	1.0756	0.365
27DAP/reference	1.0283	0.721
39DAP/reference	1.1301	0.112
41DAP/reference	1.13161	0.455
42DAP/reference	1.05097	0.658
43DAP/reference	0.98306	0.639
47DAP/reference	0.8929	0.215
52DAP/reference	2.32274	0.212
57DAP/reference	1.57581	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17578	0.966
26DAP/20DAP	1.41982
34DAP/26DAP	1.14997	0.988
51DAP/34DAP	1.05688	0.988
52DAP/51DAP	1.88812	0.103
53DAP/52DAP	0.7655	0.15
55DAP/53DAP	1.23599	0.399
57DAP/55DAP	0.62887	0.106
62DAP/57DAP	1.17081	0.678
68DAP/62DAP	1.11328	0.689
68DAP/14DAP	1.09443	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94053	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.92129	0.287
Mature Green Tomato/Ripe Tomato	1.54282
Immature Eggplant/Mature Eggplant	0.97344	0.912
Ripe Pepper/Ripe Tomato	0.7198	0.224
Mature Eggplant/Ripe Tomato	0.80786

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.99771
12-2/M82	N/A	N/A
12-4/M82	0.725	0.358
1-3/M82	N/A	N/A
2-1-1/M82	0.97862
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	0.73696	0.447
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	0.81106	0.321
IL2-6/WTpooled	1.16296	0.531
IL7-5/WTpooled	1.24115	0.75
IL7-3/WTpooled	0.96483	1
IL12-4/WTpooled	1.02426	0.891
IL1-4/WTpooled	1.01665	1
WT/WTpooled	0.92882	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	0.82585	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99257	1
DC3000/delta hrp 6h	1.03713	1
DC3000/delta hrp 12h	1.02166	1
DC3000/delta hrp 24h	0.66796	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66953	0.068
DC3000 delta B/DC3000 delta AB	0.6649	0.033

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.91081	1
Exp 36h	0.68389	0.41
Exp 60h	0.64404	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02851	1
Var 0h	0.84362	0.457
Var 12h I row2-row1	0.69336	0.338
Var 12h NI row2-row1	1.03625	0.649
Var 36h I row2-row1	1.14545	1
Var 36h NI row2-row1	1.24592	0.482
Var 60h I row2-row1	0.98408
Var 60h NI row2-row1	1.21464	0.904
Time course 0hI-0hNI	0.936	0.527
Time course 12hI-12hNI	1.07796	0.493
Time course 36hI-36hNI	0.92199	0.274
Time course 60hI-60hNI	0.17612	0.006

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)	1.58425	0.384
transgenic ySAMdc/azygous control (breaker)	0.59571	0.139
transgenic ySAMdc/azygous control (red)	1.1438	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92724	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21735	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.53453	0.096
Manapal/WT (break)	1.59175	0.183
Manapal/WT (red)	3.28163	0.15