Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2619	0.452
27DAP/17DAP	1.13609	0.881
39DAP/27DAP	1.38235	0.184
41DAP/39DAP	0.81123	0.443
42DAP/41DAP	0.84216	0.774
43DAP/42DAP	1.00201	0.934
47DAP/43DAP	0.8558	0.609
52DAP/47DAP	1.5723	0.227
57DAP/52DAP	1.25843	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76385	0.03
17DAP/reference	0.85567	0.138
27DAP/reference	0.82242	0.012
39DAP/reference	0.72999	0.012
41DAP/reference	0.76482	0.031
42DAP/reference	0.7328	0.022
43DAP/reference	0.77434
47DAP/reference	0.71992	0.007
52DAP/reference	0.83038	0.041
57DAP/reference	0.50509

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27202	0.076
27DAP/17DAP	1.07255	0.887
39DAP/27DAP	1.11603	1
41DAP/39DAP	1.06854	0.837
42DAP/41DAP	0.9644	0.753
43DAP/42DAP	0.99684	0.854
47DAP/43DAP	1.32675	0.424
52DAP/47DAP	0.80161	0.677
57DAP/52DAP	1.15071	0.601
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22197	0.201
17DAP/reference	0.99938	0.693
27DAP/reference	0.85505	0.071
39DAP/reference	0.70616	0.021
41DAP/reference	0.65612	0.011
42DAP/reference	0.75931	0.023
43DAP/reference	0.94989	0.368
47DAP/reference	0.8114	0.168
52DAP/reference	1.13777	0.428
57DAP/reference	1.05556	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65401	0.011
17DAP/reference	0.68696	0.011
27DAP/reference	0.74598	0.011
39DAP/reference	0.81658	0.076
41DAP/reference	0.76551	0.006
42DAP/reference	0.79915	0.046
43DAP/reference	0.66263	0.004
47DAP/reference	0.86255	0.087
52DAP/reference	0.92755	0.259
57DAP/reference	0.7036	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87361	0.054
17DAP/reference	0.91533	0.281
27DAP/reference	0.85965	0.092
39DAP/reference	0.88072	0.058
41DAP/reference	0.96192	0.56
42DAP/reference	0.82529	0.025
43DAP/reference	0.81556	0.057
47DAP/reference	0.83007	0.114
52DAP/reference	1.01865	1
57DAP/reference	0.8792	0.109

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16334	1
26DAP/20DAP	1.62658	0.118
34DAP/26DAP	0.93331	0.909
51DAP/34DAP	1.5441	0.1
52DAP/51DAP	1.44638	0.431
53DAP/52DAP	0.85859	0.514
55DAP/53DAP	0.9268	0.604
57DAP/55DAP	0.97298	0.854
62DAP/57DAP	0.87197	0.466
68DAP/62DAP	2.30258	0.013
68DAP/14DAP	1.78066	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96866	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.75758	0.234
Mature Green Tomato/Ripe Tomato	0.83401	0.226
Immature Eggplant/Mature Eggplant	0.64824
Ripe Pepper/Ripe Tomato	2.22549	1
Mature Eggplant/Ripe Tomato	0.71304

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.22112	1
12-2/M82	N/A	N/A
12-4/M82	1.47814	1
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	1.08098
4-1-1/M82	N/A	N/A
4-1/M82	2.40194
4-3-2/M82	1.65345	0.284
4-3/M82	N/A	N/A
5-3/M82	1.14261	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.11952
7-2/M82	N/A	N/A
9-3-2/M82	1.32637

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.37145	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.01557	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.79116	0.338
WT/WTpooled	1.19824

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	1.12334	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11761	0.914
DC3000/delta hrp 6h	0.79128	0.95
DC3000/delta hrp 12h	0.99837	1
DC3000/delta hrp 24h	1.39954	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10848	1
DC3000 delta B/DC3000 delta AB	7.59207

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.14078	1
Exp 36h	1.3245	0.693
Exp 60h	1.21361	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99909	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.19991	0.58
Var 12h NI row2-row1	1.42211	0.649
Var 36h I row2-row1	1.06815	1
Var 36h NI row2-row1	0.68636	0.549
Var 60h I row2-row1	0.88129	0.285
Var 60h NI row2-row1	0.73028	0.302
Time course 0hI-0hNI	1.08247	0.852
Time course 12hI-12hNI	0.98883	0.931
Time course 36hI-36hNI	1.53614	0.006
Time course 60hI-60hNI	2.41414	0.008

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)	0.97624	0.614
transgenic ySAMdc/azygous control (breaker)	1.23077	0.248
transgenic ySAMdc/azygous control (red)	1.12232	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05686	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.29392	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99786	1
Manapal/WT (break)	1.04111	1
Manapal/WT (red)	0.90757	0.242