Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.8.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02388	0.919
27DAP/17DAP	1.54337	0.647
39DAP/27DAP	0.92619	0.594
41DAP/39DAP	1.22089	0.638
42DAP/41DAP	1.20528	0.868
43DAP/42DAP	1.10748	1
47DAP/43DAP	1.08646	0.769
52DAP/47DAP	0.67025	0.174
57DAP/52DAP	1.02485	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92958	0.262
17DAP/reference	0.92416	0.278
27DAP/reference	1.0648	0.498
39DAP/reference	0.96605	0.638
41DAP/reference	0.79607	0.085
42DAP/reference	1.02834	0.869
43DAP/reference	1.07639	0.596
47DAP/reference	0.91402	0.148
52DAP/reference	0.94667	0.25
57DAP/reference	1.07003	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18083	0.536
27DAP/17DAP	1.00495	0.969
39DAP/27DAP	1.10851	0.422
41DAP/39DAP	0.94644	0.861
42DAP/41DAP	1.1339	0.694
43DAP/42DAP	1.13499	0.212
47DAP/43DAP	1.05367	0.873
52DAP/47DAP	0.8941	0.426
57DAP/52DAP	0.86148	0.136
57DAP/7DAP	1.3227	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13901	0.263
17DAP/reference	1.16554	0.134
27DAP/reference	0.98147	0.53
39DAP/reference	0.97729	0.64
41DAP/reference	1.01002	0.778
42DAP/reference	1.42039	0.018
43DAP/reference	1.42958	0.023
47DAP/reference	1.25916	0.161
52DAP/reference	1.06155	0.328
57DAP/reference	1.19876	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00445	0.993
17DAP/reference	1.00574	0.711
27DAP/reference	0.99493	0.663
39DAP/reference	0.95729	0.381
41DAP/reference	1.12522	0.48
42DAP/reference	0.91407	0.108
43DAP/reference	1.06882	0.662
47DAP/reference	0.89526	0.069
52DAP/reference	0.98898	0.576
57DAP/reference	0.82511	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96446	0.526
17DAP/reference	1.0358	0.934
27DAP/reference	0.905	0.397
39DAP/reference	0.94493	0.069
41DAP/reference	0.95672	0.512
42DAP/reference	0.84941	0.041
43DAP/reference	0.86253	0.098
47DAP/reference	0.97948	0.538
52DAP/reference	1.00105	0.888
57DAP/reference	0.84917	0.024

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.72736	0.807
26DAP/20DAP	0.95003	1
34DAP/26DAP	1.21384	0.819
51DAP/34DAP	2.12453	0.029
52DAP/51DAP	0.6933	0.151
53DAP/52DAP	1.45017	0.104
55DAP/53DAP	0.48084	0.023
57DAP/55DAP	1.05131	0.927
62DAP/57DAP	1.77422	0.003
68DAP/62DAP	0.76379	0.082
68DAP/14DAP	1.56592	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.63412	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.37025	0.078
Mature Green Tomato/Ripe Tomato	0.95407	0.569
Immature Eggplant/Mature Eggplant	1.76192	0.05
Ripe Pepper/Ripe Tomato	6.37917	0.256
Mature Eggplant/Ripe Tomato	1.37194	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.85945	0.69
1-1-2/M82	1.23378	1
12-2/M82	1.00303	1
12-4/M82	0.81049	0.262
1-3/M82	1.32898
2-1-1/M82	0.93921	1
2-1/M82	N/A	N/A
2-6/M82	1.30839	0.329
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	1.3429	0.246
4-3/M82	1.06119
5-3/M82	1.02885	1
6-2/M82	N/A	N/A
6-3/M82	0.8861	1
7-1/M82	0.9972
7-2/M82	1.35457
9-3-2/M82	1.35577	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.24174	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.87631	0.554
IL1-4/WTpooled	1.1104	0.317
WT/WTpooled	0.90796

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	0.7421	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06263	0.724
DC3000/delta hrp 6h	1.07594	0.777
DC3000/delta hrp 12h	1.01755	1
DC3000/delta hrp 24h	0.99816	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.58065	0.025
DC3000 delta B/DC3000 delta AB	0.75014	0.063

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02131	1
Exp 36h	1.05538	1
Exp 60h	1.2596	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03186	1
Var 0h	0.80599	0.933
Var 12h I row2-row1	0.94914	0.856
Var 12h NI row2-row1	0.85798	0.627
Var 36h I row2-row1	0.87322	1
Var 36h NI row2-row1	0.98935	0.852
Var 60h I row2-row1	0.79907	0.439
Var 60h NI row2-row1	0.97219	1
Time course 0hI-0hNI	0.88812	0.256
Time course 12hI-12hNI	0.90944	0.295
Time course 36hI-36hNI	0.99689	0.768
Time course 60hI-60hNI	0.65012	0.011

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)	0.90678	0.297
transgenic ySAMdc/azygous control (breaker)	1.01289	1
transgenic ySAMdc/azygous control (red)	0.9535	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07387	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71593	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.27283	0.105
Manapal/WT (break)	1.16134	0.381
Manapal/WT (red)	1.16773	0.413