Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.18.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9721	0.779
27DAP/17DAP	1.30914	0.735
39DAP/27DAP	1.1657	0.899
41DAP/39DAP	1.03206	0.806
42DAP/41DAP	0.93034	1
43DAP/42DAP	1.07025	1
47DAP/43DAP	1.16625	0.793
52DAP/47DAP	1.00592	0.843
57DAP/52DAP	1.07162	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99563	0.743
17DAP/reference	0.9942	0.858
27DAP/reference	0.9806	0.525
39DAP/reference	1.04598	0.098
41DAP/reference	1.04718	0.312
42DAP/reference	1.02714	0.431
43DAP/reference	0.98772	0.763
47DAP/reference	0.99453	0.602
52DAP/reference	1.05646	0.407
57DAP/reference	0.91104	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00144	1
27DAP/17DAP	0.96928	0.854
39DAP/27DAP	1.08801	0.534
41DAP/39DAP	1.12717	0.799
42DAP/41DAP	1.06575	0.622
43DAP/42DAP	1.03499	0.627
47DAP/43DAP	1.05666	0.857
52DAP/47DAP	1.02018	0.945
57DAP/52DAP	0.99325	0.845
57DAP/7DAP	1.02888	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91412	0.071
17DAP/reference	0.96553	0.082
27DAP/reference	0.89545	0.014
39DAP/reference	0.96126	0.146
41DAP/reference	0.96836	0.412
42DAP/reference	0.92644	0.066
43DAP/reference	0.95735	0.266
47DAP/reference	0.88064	0.026
52DAP/reference	0.9314	0.077
57DAP/reference	1.01102	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99907	0.993
17DAP/reference	1.03987	0.406
27DAP/reference	0.9484	0.24
39DAP/reference	0.93422	0.132
41DAP/reference	1.01374	1
42DAP/reference	0.96748	0.355
43DAP/reference	1.05628	0.466
47DAP/reference	0.96955	0.154
52DAP/reference	0.98446	0.5
57DAP/reference	1.06303	0.363

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93599	0.23
17DAP/reference	0.98696	0.696
27DAP/reference	1.01724	0.903
39DAP/reference	0.92693	0.022
41DAP/reference	0.94098	0.148
42DAP/reference	0.86753	0.016
43DAP/reference	0.91671	0.073
47DAP/reference	0.96682	0.296
52DAP/reference	0.89961	0.153
57DAP/reference	0.83514	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00291	1
26DAP/20DAP	0.90942	0.512
34DAP/26DAP	0.99332	1
51DAP/34DAP	0.93826	0.563
52DAP/51DAP	1.12205	0.094
53DAP/52DAP	1.08161	0.489
55DAP/53DAP	1.00332	0.917
57DAP/55DAP	1.15949	0.779
62DAP/57DAP	0.95091	0.681
68DAP/62DAP	1.06108	0.977
68DAP/14DAP	0.92339	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.99508	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.42318
Mature Green Tomato/Ripe Tomato	1.22646	0.299
Immature Eggplant/Mature Eggplant	1.0977	0.528
Ripe Pepper/Ripe Tomato	0.79603	0.224
Mature Eggplant/Ripe Tomato	0.92721	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9266	0.944
1-1-2/M82	1.03133
12-2/M82	1.15133	1
12-4/M82	1.06206	1
1-3/M82	0.92453	1
2-1-1/M82	1.09327	0.689
2-1/M82	1.10693	1
2-6/M82	0.96307	1
3-2/M82	0.98448
4-1-1/M82	0.88104	1
4-1/M82	1.29805	1
4-3-2/M82	0.973	1
4-3/M82	0.99765	1
5-3/M82	0.97371	0.49
6-2/M82	1.02833	1
6-3/M82	1.02392	1
7-1/M82	1.12241	0.598
7-2/M82	0.94041	0.469
9-3-2/M82	1.04303	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.97604	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02303	0.921
DC3000/delta hrp 6h	1.08473	1
DC3000/delta hrp 12h	1.00958	1
DC3000/delta hrp 24h	1.02744	0.76

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.96424	0.803
DC3000 delta B/DC3000 delta AB	0.94757	0.47

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86728	1
Exp 36h	1.17623	1
Exp 60h	1.11345	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9706	1
Var 0h	0.99737	1
Var 12h I row2-row1	1.10864	0.196
Var 12h NI row2-row1	0.93679	0.82
Var 36h I row2-row1	1.01444	1
Var 36h NI row2-row1	0.96051	0.706
Var 60h I row2-row1	1.34309	0.562
Var 60h NI row2-row1	1.10642	1
Time course 0hI-0hNI	1.05329	0.852
Time course 12hI-12hNI	1.02346	0.82
Time course 36hI-36hNI	0.93201	0.179
Time course 60hI-60hNI	1.03786	0.495

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)	0.99272	0.931
transgenic ySAMdc/azygous control (breaker)	0.90161	0.49
transgenic ySAMdc/azygous control (red)	0.99496	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97922	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93333	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89768	1
Manapal/WT (break)	0.86577	0.299
Manapal/WT (red)	0.77161	0.181