Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.14.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96778	0.76
27DAP/17DAP	1.03554	0.927
39DAP/27DAP	1.27054	0.546
41DAP/39DAP	0.94096	0.711
42DAP/41DAP	1.08056	0.994
43DAP/42DAP	0.92083	0.813
47DAP/43DAP	0.92521	0.705
52DAP/47DAP	1.685	0.493
57DAP/52DAP	0.93061	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92788	0.182
17DAP/reference	0.90703	0.014
27DAP/reference	0.91967	0.176
39DAP/reference	0.92792	0.194
41DAP/reference	0.8566	0.008
42DAP/reference	0.98534	0.398
43DAP/reference	0.99755	0.904
47DAP/reference	1.00044	0.674
52DAP/reference	1.07803	0.354
57DAP/reference	1.09677	0.141

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13218	0.34
27DAP/17DAP	0.99666	0.969
39DAP/27DAP	0.99576	1
41DAP/39DAP	1.1564	0.753
42DAP/41DAP	0.88552	0.399
43DAP/42DAP	1.06593	0.273
47DAP/43DAP	0.98086	0.933
52DAP/47DAP	1.04346	0.856
57DAP/52DAP	0.9595	0.612
57DAP/7DAP	1.46202	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88878	0.146
17DAP/reference	0.83642	0.011
27DAP/reference	0.71817	0.01
39DAP/reference	0.73526	0.011
41DAP/reference	0.71487	0.016
42DAP/reference	0.71015	0.012
43DAP/reference	0.72249	0.014
47DAP/reference	0.88465	0.222
52DAP/reference	0.68036	0.012
57DAP/reference	0.94977	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93932	0.426
17DAP/reference	0.93106	0.253
27DAP/reference	0.86529	0.097
39DAP/reference	0.86612	0.019
41DAP/reference	0.97949	0.472
42DAP/reference	0.86173	0.023
43DAP/reference	1.07514	0.509
47DAP/reference	0.87239	0.016
52DAP/reference	0.98338	0.5
57DAP/reference	0.82447	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80436	0.052
17DAP/reference	0.9981	0.825
27DAP/reference	0.78216	0.038
39DAP/reference	0.73744	0.021
41DAP/reference	0.80513	0.033
42DAP/reference	0.80991	0.134
43DAP/reference	0.79934	0.066
47DAP/reference	1.04578	0.63
52DAP/reference	0.82832	0.238
57DAP/reference	1.10829	0.531

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92621	0.915
26DAP/20DAP	1.00142	1
34DAP/26DAP	0.9646	0.917
51DAP/34DAP	1.09377	0.627
52DAP/51DAP	0.97365	1
53DAP/52DAP	1.07133	0.753
55DAP/53DAP	1.03644	0.994
57DAP/55DAP	1.10435	0.324
62DAP/57DAP	1.10385	0.678
68DAP/62DAP	0.98168	0.81
68DAP/14DAP	1.19336	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94339	0.211

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05405	0.666
Mature Green Tomato/Ripe Tomato	0.71665	0.02
Immature Eggplant/Mature Eggplant	1.13401	0.215
Ripe Pepper/Ripe Tomato	1.19906	1
Mature Eggplant/Ripe Tomato	0.76583	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.13552	0.742
1-1-2/M82	0.87277	1
12-2/M82	1.06437	1
12-4/M82	0.81913	1
1-3/M82	1.11914	1
2-1-1/M82	0.95682	0.92
2-1/M82	0.81232
2-6/M82	1.032	0.695
3-2/M82	1.02367	0.967
4-1-1/M82	0.91905	1
4-1/M82	0.66339
4-3-2/M82	0.83244	0.698
4-3/M82	0.82956	0.72
5-3/M82	0.98514
6-2/M82	0.76391	0.481
6-3/M82	0.92877	0.982
7-1/M82	0.7518	0.466
7-2/M82	1.09205	0.385
9-3-2/M82	1.01606	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.2637	0.395
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.74114	0.294
IL12-4/WTpooled	0.95804	0.71
IL1-4/WTpooled	0.94668
WT/WTpooled	1.06007	0.957

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	1.00898	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03349	0.921
DC3000/delta hrp 6h	0.97384	0.95
DC3000/delta hrp 12h	1.13357	1
DC3000/delta hrp 24h	1.13555	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16831	0.042
DC3000 delta B/DC3000 delta AB	1.04737	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9888	1
Exp 36h	1.07001	0.693
Exp 60h	1.15115	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97106	1
Var 0h	1.12476	0.936
Var 12h I row2-row1	0.93626	0.705
Var 12h NI row2-row1	0.8115	0.627
Var 36h I row2-row1	0.99846	1
Var 36h NI row2-row1	0.80995	0.549
Var 60h I row2-row1	0.97005	0.952
Var 60h NI row2-row1	1.02298	1
Time course 0hI-0hNI	1.11986	0.246
Time course 12hI-12hNI	1.01981	0.811
Time course 36hI-36hNI	1.14562	0.035
Time course 60hI-60hNI	1.99773	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)	0.97828	0.454
transgenic ySAMdc/azygous control (breaker)	0.59817	0.132
transgenic ySAMdc/azygous control (red)	0.93281	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09467	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85179	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90463	1
Manapal/WT (break)	1.01679	1
Manapal/WT (red)	0.46596	0.181