Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.9.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26998	0.414
27DAP/17DAP	0.91792	0.863
39DAP/27DAP	1.41596	0.606
41DAP/39DAP	1.16361	0.691
42DAP/41DAP	1.284	0.336
43DAP/42DAP	1.29087	0.746
47DAP/43DAP	0.73913	0.228
52DAP/47DAP	1.38602	0.608
57DAP/52DAP	1.33318	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05492	0.788
17DAP/reference	1.09288	0.104
27DAP/reference	1.20557	0.069
39DAP/reference	1.26851	0.014
41DAP/reference	1.25649	0.026
42DAP/reference	0.99583	0.567
43DAP/reference	1.12135	0.126
47DAP/reference	1.08982	0.433
52DAP/reference	1.16996	0.134
57DAP/reference	1.09607	0.079

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.57341	0.04
27DAP/17DAP	0.91221	0.58
39DAP/27DAP	1.01032	1
41DAP/39DAP	1.12602	0.579
42DAP/41DAP	0.91028	0.374
43DAP/42DAP	0.94267	0.447
47DAP/43DAP	0.97244	0.857
52DAP/47DAP	1.02028	0.986
57DAP/52DAP	1.09056	0.643
57DAP/7DAP	1.24999	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0681	0.857
17DAP/reference	1.39377	0.112
27DAP/reference	1.1201	0.664
39DAP/reference	1.22495	0.314
41DAP/reference	1.1671	0.336
42DAP/reference	1.09423	0.233
43DAP/reference	1.22611	0.14
47DAP/reference	1.14628	0.514
52DAP/reference	1.18014	0.113
57DAP/reference	1.14995	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95594	0.532
17DAP/reference	1.31359	0.036
27DAP/reference	1.34986	0.02
39DAP/reference	1.2536	0.022
41DAP/reference	1.19548	0.032
42DAP/reference	1.08785	0.18
43DAP/reference	1.2024	0.146
47DAP/reference	1.19103	0.061
52DAP/reference	1.29254	0.015
57DAP/reference	1.02902	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01928	1
17DAP/reference	0.79686	0.305
27DAP/reference	1.19645	0.062
39DAP/reference	1.2442	0.078
41DAP/reference	1.10446	0.605
42DAP/reference	1.30169	0.024
43DAP/reference	1.17214	0.296
47DAP/reference	1.45046	0.007
52DAP/reference	1.1236	0.851
57DAP/reference	1.36807	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2997	0.786
26DAP/20DAP	1.36011	0.21
34DAP/26DAP	1.19081	0.154
51DAP/34DAP	1.30546	0.326
52DAP/51DAP	0.929	1
53DAP/52DAP	1.10525	0.502
55DAP/53DAP	1.01445	0.939
57DAP/55DAP	0.97208	0.823
62DAP/57DAP	0.91336	0.681
68DAP/62DAP	1.23957	0.375
68DAP/14DAP	1.20803	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.93612	0.017

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.80879	0.286
Mature Green Tomato/Ripe Tomato	1.48553	0.523
Immature Eggplant/Mature Eggplant	1.90984	0.05
Ripe Pepper/Ripe Tomato	0.86185	1
Mature Eggplant/Ripe Tomato	1.28073

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	0.87317
1-3/M82	N/A	N/A
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	N/A	N/A
5-3/M82	0.87713	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	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97105	1
IL2-6/WTpooled	1.15039	0.395
IL7-5/WTpooled	0.94383	1
IL7-3/WTpooled	1.04102	1
IL12-4/WTpooled	1.09324	0.595
IL1-4/WTpooled	1.00971	1
WT/WTpooled	0.97903	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	0.99052	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02892	0.921
DC3000/delta hrp 6h	1.01197	1
DC3000/delta hrp 12h	1.0605	1
DC3000/delta hrp 24h	1.17593	0.123

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.87663
DC3000 delta B/DC3000 delta AB	1.22847	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97841	1
Exp 36h	1.30354	1
Exp 60h	1.38971	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03	1
Var 0h	0.39587	0.244
Var 12h I row2-row1	1.14786	0.506
Var 12h NI row2-row1	1.0178	1
Var 36h I row2-row1	1.11712	0.291
Var 36h NI row2-row1	0.55104	0.225
Var 60h I row2-row1	0.7365	0.439
Var 60h NI row2-row1	0.89831	0.818
Time course 0hI-0hNI	0.9121	0.349
Time course 12hI-12hNI	1.00376	1
Time course 36hI-36hNI	1.25233	0.021
Time course 60hI-60hNI	1.20925	0.042

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)	1.05038	0.541
transgenic ySAMdc/azygous control (breaker)	0.93453	1
transgenic ySAMdc/azygous control (red)	0.94028	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00116	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81622	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.7695	0.172
Manapal/WT (break)	0.86864	1
Manapal/WT (red)	0.82311	0.315