Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.863	0.324
27DAP/17DAP	1.46045	0.813
39DAP/27DAP	1.38178	0.593
41DAP/39DAP	0.91502	0.6
42DAP/41DAP	1.21505	0.587
43DAP/42DAP	1.04854	1
47DAP/43DAP	0.71275	0.225
52DAP/47DAP	1.32745	0.696
57DAP/52DAP	1.30579	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13096	0.421
17DAP/reference	0.99332	0.858
27DAP/reference	0.96426	0.514
39DAP/reference	0.89561	0.194
41DAP/reference	0.8998	0.267
42DAP/reference	0.96401	0.268
43DAP/reference	1.07959	0.382
47DAP/reference	1.02634	0.989
52DAP/reference	1.15009	0.286
57DAP/reference	1.14211	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93334	0.428
27DAP/17DAP	1.1569	0.218
39DAP/27DAP	0.93388	0.648
41DAP/39DAP	1.09408	0.753
42DAP/41DAP	0.94964	0.637
43DAP/42DAP	1.07386	0.513
47DAP/43DAP	0.98274	0.911
52DAP/47DAP	0.92819	0.522
57DAP/52DAP	1.08391	0.65
57DAP/7DAP	0.97421

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02607	1
17DAP/reference	0.73564	0.049
27DAP/reference	1.06042	0.8
39DAP/reference	0.75665	0.017
41DAP/reference	1.05384	0.524
42DAP/reference	1.05501	0.828
43DAP/reference	1.17355	0.974
47DAP/reference	0.95417	0.504
52DAP/reference	1.09294	1
57DAP/reference	1.21198	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92611	0.412
17DAP/reference	0.93321	0.287
27DAP/reference	1.00178	0.663
39DAP/reference	0.97785	0.497
41DAP/reference	1.02566	0.781
42DAP/reference	0.98612	0.594
43DAP/reference	0.88802	0.191
47DAP/reference	0.88478	0.032
52DAP/reference	1.11757	0.05
57DAP/reference	0.96847	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11439	0.659
17DAP/reference	0.98837	0.778
27DAP/reference	1.07103	0.575
39DAP/reference	0.9205	0.43
41DAP/reference	1.18181
42DAP/reference	1.22576	0.443
43DAP/reference	1.19082	0.349
47DAP/reference	1.01058	1
52DAP/reference	0.78514	0.247
57DAP/reference	1.19422	0.064

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00865	1
26DAP/20DAP	1.55543	0.142
34DAP/26DAP	1.22613	0.304
51DAP/34DAP	1.26026
52DAP/51DAP	0.96003	1
53DAP/52DAP	1.07136	0.882
55DAP/53DAP	0.90522	0.176
57DAP/55DAP	1.37794	0.051
62DAP/57DAP	0.66204	0.007
68DAP/62DAP	0.99535	0.914
68DAP/14DAP	1.78586	0.057

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.57671	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.39904	0.107
Mature Green Tomato/Ripe Tomato	1.55459	0.331
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.41993	1
Mature Eggplant/Ripe Tomato	0.94441	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95742	0.944
1-1-2/M82	0.92891
12-2/M82	0.76114
12-4/M82	0.80744
1-3/M82	1.35679	0.479
2-1-1/M82	0.96418	0.465
2-1/M82	0.88135
2-6/M82	1.06705	0.505
3-2/M82	N/A	N/A
4-1-1/M82	1.06059	1
4-1/M82	1.07015
4-3-2/M82	1.30636
4-3/M82	1.20941	1
5-3/M82	1.02282	1
6-2/M82	N/A	N/A
6-3/M82	0.81351	0.982
7-1/M82	0.95308
7-2/M82	1.16817	0.385
9-3-2/M82	1.25439

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72968	0.243
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.22847
IL7-3/WTpooled	0.71023
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.88636	0.562
WT/WTpooled	2.45638	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	1.4713	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9588	1
DC3000/delta hrp 6h	1.14842	1
DC3000/delta hrp 12h	1.00981	1
DC3000/delta hrp 24h	0.75991	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.54635	0.229
DC3000 delta B/DC3000 delta AB	1.17477	0.261

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03635	1
Exp 36h	0.96047	0.943
Exp 60h	0.88696	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01665
Var 0h	0.61372	1
Var 12h I row2-row1	0.87374	0.627
Var 12h NI row2-row1	1.06904	1
Var 36h I row2-row1	1.11913	0.489
Var 36h NI row2-row1	0.98572	0.852
Var 60h I row2-row1	0.82719
Var 60h NI row2-row1	0.88677	0.359
Time course 0hI-0hNI	0.89582	0.157
Time course 12hI-12hNI	1.02443	0.747
Time course 36hI-36hNI	1.23289	0.039
Time course 60hI-60hNI	1.70894	0.009

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)	1.02068	0.798
transgenic ySAMdc/azygous control (breaker)	1.21897	0.172
transgenic ySAMdc/azygous control (red)	0.97571	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98847	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24397	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.30311	1
Manapal/WT (break)	1.08734	1
Manapal/WT (red)	1.39505	0.222