Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00672	0.867
27DAP/17DAP	0.99663	0.945
39DAP/27DAP	1.77526	0.039
41DAP/39DAP	0.68821	0.101
42DAP/41DAP	1.2942	0.802
43DAP/42DAP	1.26917	1
47DAP/43DAP	0.3866	0.049
52DAP/47DAP	1.4417	0.538
57DAP/52DAP	1.00755	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81698	0.054
17DAP/reference	0.76148	0.028
27DAP/reference	0.93306	0.471
39DAP/reference	0.75081	0.036
41DAP/reference	0.69045	0.01
42DAP/reference	0.78368	0.001
43DAP/reference	0.95216	0.48
47DAP/reference	0.9433	0.191
52DAP/reference	1.1142	0.096
57DAP/reference	1.17711	0.076

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.02589	0.168
27DAP/17DAP	1.18489	0.9
39DAP/27DAP	1.13726	0.447
41DAP/39DAP	1.16455	0.88
42DAP/41DAP	0.82104	0.098
43DAP/42DAP	0.76231	0.101
47DAP/43DAP	1.06393	0.951
52DAP/47DAP	1.40025	0.258
57DAP/52DAP	1.38131	0.197
57DAP/7DAP	0.83554

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.58069	0.042
17DAP/reference	1.95451	0.007
27DAP/reference	1.61598	0.008
39DAP/reference	2.23477	0.005
41DAP/reference	2.20044	0.012
42DAP/reference	2.10884	0.007
43DAP/reference	2.43012	0.007
47DAP/reference	1.54332	0.178
52DAP/reference	1.74182	0.013
57DAP/reference	1.7119	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68852	0.008
17DAP/reference	0.68029	0.005
27DAP/reference	0.77789	0.033
39DAP/reference	0.80876	0.06
41DAP/reference	0.84503	0.024
42DAP/reference	0.89661	0.015
43DAP/reference	0.61368	0.007
47DAP/reference	0.7493	0.06
52DAP/reference	0.87619	0.047
57DAP/reference	0.70332	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.88421	0.034
17DAP/reference	1.1218	0.824
27DAP/reference	1.78325	0.035
39DAP/reference	1.68316	0.025
41DAP/reference	1.71031	0.017
42DAP/reference	1.65421	0.031
43DAP/reference	1.67252	0.071
47DAP/reference	0.94453	0.306
52DAP/reference	1.49004	0.179
57DAP/reference	1.36037	0.279

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.82052	0.786
26DAP/20DAP	0.94824	1
34DAP/26DAP	0.88884	0.944
51DAP/34DAP	1.03048	0.949
52DAP/51DAP	1.86834	0.197
53DAP/52DAP	1.11432	0.845
55DAP/53DAP	0.93067	0.735
57DAP/55DAP	0.89059	0.527
62DAP/57DAP	1.05906	0.994
68DAP/62DAP	1.23572	0.971
68DAP/14DAP	2.30211	0.041

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.93211	0.151

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.11972
Mature Green Tomato/Ripe Tomato	0.82804	0.347
Immature Eggplant/Mature Eggplant	2.12118
Ripe Pepper/Ripe Tomato	0.71123	1
Mature Eggplant/Ripe Tomato	1.08014	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.12248	0.611
1-3/M82	0.99575
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.85346
5-3/M82	1.29631	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.93569	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.80238	0.247
IL2-6/WTpooled	0.63513	0.383
IL7-5/WTpooled	0.65624	1
IL7-3/WTpooled	0.90275	1
IL12-4/WTpooled	0.99525	1
IL1-4/WTpooled	0.72683	0.699
WT/WTpooled	1.01602	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	1.19367	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08892	0.724
DC3000/delta hrp 6h	0.91612	0.95
DC3000/delta hrp 12h	0.8893	1
DC3000/delta hrp 24h	1.05806	0.397

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.4981

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94816	1
Exp 36h	1.17358	1
Exp 60h	1.28478	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04996	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.20221	0.473
Var 12h NI row2-row1	1.05085	1
Var 36h I row2-row1	0.93458	1
Var 36h NI row2-row1	0.97481	0.852
Var 60h I row2-row1	0.95948	0.832
Var 60h NI row2-row1	0.94607	0.904
Time course 0hI-0hNI	0.95631	0.699
Time course 12hI-12hNI	0.97555	0.874
Time course 36hI-36hNI	1.09954	0.355
Time course 60hI-60hNI	0.97035	0.646

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)	1.02963	0.863
transgenic ySAMdc/azygous control (breaker)	1.19633	0.178
transgenic ySAMdc/azygous control (red)	1.03663	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04132	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.12219	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83262	1
Manapal/WT (break)	0.88428	0.333
Manapal/WT (red)	0.91804	0.315