Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.19.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76097	0.141
27DAP/17DAP	1.40717	0.849
39DAP/27DAP	1.03482	1
41DAP/39DAP	0.84318	0.457
42DAP/41DAP	1.07352	0.938
43DAP/42DAP	1.08639	1
47DAP/43DAP	0.83144	0.48
52DAP/47DAP	0.95832	0.854
57DAP/52DAP	0.89757	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53847	0.017
17DAP/reference	1.50057	0.051
27DAP/reference	1.28134	0.135
39DAP/reference	1.411	0.174
41DAP/reference	1.60676	0.041
42DAP/reference	1.10834	0.191
43DAP/reference	1.12702	0.403
47DAP/reference	1.37208	0.008
52DAP/reference	1.1117	0.912
57DAP/reference	1.19645	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90098	0.526
27DAP/17DAP	1.32614	0.37
39DAP/27DAP	0.81407	0.382
41DAP/39DAP	0.93686	0.885
42DAP/41DAP	0.98791	0.774
43DAP/42DAP	1.21892	0.212
47DAP/43DAP	1.0937	0.969
52DAP/47DAP	0.8276	0.222
57DAP/52DAP	0.97727	0.753
57DAP/7DAP	1.13032	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55323	0.073
17DAP/reference	0.54519	0.011
27DAP/reference	0.57386	0.01
39DAP/reference	0.83545	0.064
41DAP/reference	0.8469	0.082
42DAP/reference	1.18501	0.308
43DAP/reference	1.36019	0.032
47DAP/reference	1.39165	0.421
52DAP/reference	0.77935	0.021
57DAP/reference	0.93959	0.328

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98614	0.831
17DAP/reference	1.23465	0.264
27DAP/reference	1.17837	0.23
39DAP/reference	1.22921	0.412
41DAP/reference	1.03294	1
42DAP/reference	1.11795	0.621
43DAP/reference	1.20964	0.417
47DAP/reference	1.09975	0.353
52DAP/reference	1.2887	0.069
57DAP/reference	1.52971	0.07

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53375	0.029
17DAP/reference	0.92463	0.426
27DAP/reference	0.53185	0.031
39DAP/reference	0.66186	0.026
41DAP/reference	0.7131	0.04
42DAP/reference	2.02917	0.019
43DAP/reference	2.14671	0.007
47DAP/reference	1.2143	0.228
52DAP/reference	1.9368	0.077
57DAP/reference	1.04158	0.933

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.57278	0.945
26DAP/20DAP	0.7577	1
34DAP/26DAP	1.1567	0.819
51DAP/34DAP	2.81543	0.377
52DAP/51DAP	1.05706	1
53DAP/52DAP	0.92868	0.79
55DAP/53DAP	0.63742	0.252
57DAP/55DAP	1.0385	0.955
62DAP/57DAP	0.85714	0.466
68DAP/62DAP	1.00556	0.914
68DAP/14DAP	1.03529

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2515	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.93023	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.18261	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11695
1-1-2/M82	1.02465	1
12-2/M82	N/A	N/A
12-4/M82	0.8497	0.298
1-3/M82	1.09771	0.479
2-1-1/M82	0.84349
2-1/M82	N/A	N/A
2-6/M82	1.19053	0.364
3-2/M82	0.7428
4-1-1/M82	1.08556
4-1/M82	0.87789
4-3-2/M82	N/A	N/A
4-3/M82	1.24657
5-3/M82	0.94416	1
6-2/M82	1.15047	1
6-3/M82	1.22263
7-1/M82	N/A	N/A
7-2/M82	1.27599	0.282
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.58555	0.277
IL2-6/WTpooled	0.78548	1
IL7-5/WTpooled	0.96806	1
IL7-3/WTpooled	0.98397	1
IL12-4/WTpooled	1.01495	1
IL1-4/WTpooled	1.20491	1
WT/WTpooled	1.07175	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	1.25966	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07282	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.68581	1
DC3000/delta hrp 24h	0.87088	0.264

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68229	0.047
DC3000 delta B/DC3000 delta AB	0.9292	0.619

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00007	1
Var 0h	0.93018	1
Var 12h I row2-row1	0.95541	0.856
Var 12h NI row2-row1	1.29891	0.281
Var 36h I row2-row1	1.16945	0.601
Var 36h NI row2-row1	1.14813	1
Var 60h I row2-row1	0.81797	0.439
Var 60h NI row2-row1	1.03135	1
Time course 0hI-0hNI	0.94203	0.629
Time course 12hI-12hNI	0.91747	0.217
Time course 36hI-36hNI	0.85175	0.031
Time course 60hI-60hNI	0.79181	0.026

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.1281	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02044	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26587	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.35472	0.222