Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.53217	0.09
27DAP/17DAP	1.03297	1
39DAP/27DAP	1.17068	1
41DAP/39DAP	0.70801	0.112
42DAP/41DAP	0.81771	0.774
43DAP/42DAP	1.01372	0.937
47DAP/43DAP	1.00541	0.972
52DAP/47DAP	0.98293	0.87
57DAP/52DAP	1.20109	0.72

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06792	1
17DAP/reference	1.23329	0.154
27DAP/reference	1.66163	0.01
39DAP/reference	0.89479	0.284
41DAP/reference	0.83116	0.154
42DAP/reference	1.12854	0.21
43DAP/reference	0.82648	0.113
47DAP/reference	1.39298	0.018
52DAP/reference	1.21417	0.242
57DAP/reference	1.39264	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7434	0.07
27DAP/17DAP	1.18034	0.488
39DAP/27DAP	0.78876	0.103
41DAP/39DAP	0.71839	0.193
42DAP/41DAP	1.20531	0.446
43DAP/42DAP	1.01571	1
47DAP/43DAP	0.90054	0.516
52DAP/47DAP	1.02621	0.973
57DAP/52DAP	0.88438	0.395
57DAP/7DAP	0.64058	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10834	0.813
17DAP/reference	1.07553	0.822
27DAP/reference	1.11342	0.804
39DAP/reference	1.17449	0.114
41DAP/reference	1.19703	0.303
42DAP/reference	1.07975	0.686
43DAP/reference	0.9581	0.368
47DAP/reference	1.23624	0.145
52DAP/reference	1.38331	0.026
57DAP/reference	1.42517	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95466	0.564
17DAP/reference	1.19584	0.257
27DAP/reference	1.37424	0.192
39DAP/reference	1.07216	0.705
41DAP/reference	0.99267	0.601
42DAP/reference	1.13915	0.214
43DAP/reference	0.73743	0.06
47DAP/reference	1.05085	0.751
52DAP/reference	1.17339	0.596
57DAP/reference	0.62863	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03886	0.903
17DAP/reference	1.18747	0.317
27DAP/reference	1.39958	0.033
39DAP/reference	0.9399	0.393
41DAP/reference	1.24831	0.369
42DAP/reference	0.92433	0.552
43DAP/reference	1.03918	0.827
47DAP/reference	0.98292	0.509
52DAP/reference	1.14972	0.575
57DAP/reference	1.7128	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96838	1
26DAP/20DAP	0.80407	0.512
34DAP/26DAP	0.93014	0.509
51DAP/34DAP	1.04409	0.909
52DAP/51DAP	1.00022	1
53DAP/52DAP	1.00206	1
55DAP/53DAP	0.81649	0.263
57DAP/55DAP	1.14935	0.947
62DAP/57DAP	1.39967	0.098
68DAP/62DAP	1.94943	0.046
68DAP/14DAP	2.65886	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51571	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.32326	0.058
Mature Green Tomato/Ripe Tomato	1.12376	0.478
Immature Eggplant/Mature Eggplant	0.5348	0.062
Ripe Pepper/Ripe Tomato	1.03066	1
Mature Eggplant/Ripe Tomato	1.37065	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.76297	0.841
1-1-2/M82	1.12821	1
12-2/M82	0.94197	1
12-4/M82	1.076	1
1-3/M82	2.05208	0.248
2-1-1/M82	1.16178	1
2-1/M82	0.8166	0.345
2-6/M82	0.81899	0.501
3-2/M82	1.3607
4-1-1/M82	1.23907	1
4-1/M82	1.27857	1
4-3-2/M82	1.03279	1
4-3/M82	1.12102	1
5-3/M82	0.91549	1
6-2/M82	1.16545	1
6-3/M82	1.04574	1
7-1/M82	1.19194	1
7-2/M82	1.1729	1
9-3-2/M82	1.15699	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99076	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03868	1
IL12-4/WTpooled	1.15533	0.525
IL1-4/WTpooled	1.23312	1
WT/WTpooled	0.99739	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	0.67745	0.201

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08028	0.875
DC3000/delta hrp 6h	1.0385	1
DC3000/delta hrp 12h	0.97428	1
DC3000/delta hrp 24h	1.08685	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44131	0.024
DC3000 delta B/DC3000 delta AB	0.48163	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01817	1
Exp 36h	0.79259	0.449
Exp 60h	0.9088	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99641	1
Var 0h	1.11788	0.259
Var 12h I row2-row1	0.84067	0.318
Var 12h NI row2-row1	0.96033	0.82
Var 36h I row2-row1	1.08664	1
Var 36h NI row2-row1	1.21871	1
Var 60h I row2-row1	1.00214	1
Var 60h NI row2-row1	1.07802	0.904
Time course 0hI-0hNI	1.05928	0.799
Time course 12hI-12hNI	0.89099	0.157
Time course 36hI-36hNI	0.72259	0.023
Time course 60hI-60hNI	0.13445	0.005

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)	1.04411	0.612
transgenic ySAMdc/azygous control (breaker)	0.78267	0.173
transgenic ySAMdc/azygous control (red)	0.77338	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94037	0.486

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.94095	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.9332	1
Manapal/WT (break)	0.90696	1
Manapal/WT (red)	1.26341	0.15