Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92734	0.578
27DAP/17DAP	0.80683	0.551
39DAP/27DAP	1.51705	0.219
41DAP/39DAP	0.96467	0.772
42DAP/41DAP	0.95163	1
43DAP/42DAP	0.90527	0.684
47DAP/43DAP	0.99731	0.851
52DAP/47DAP	1.26531	0.449
57DAP/52DAP	1.33117	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93309	0.284
17DAP/reference	0.90534	0.138
27DAP/reference	1.13349	0.33
39DAP/reference	0.96936	0.624
41DAP/reference	0.95135	0.434
42DAP/reference	0.91061	0.056
43DAP/reference	0.9904	0.82
47DAP/reference	0.99173	0.535
52DAP/reference	0.97036	0.438
57DAP/reference	1.06182	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97963	0.732
27DAP/17DAP	1.15154	0.557
39DAP/27DAP	1.1408	0.514
41DAP/39DAP	0.9876	0.934
42DAP/41DAP	1.20711	0.134
43DAP/42DAP	1.24836	0.024
47DAP/43DAP	0.99628	0.971
52DAP/47DAP	0.84849	0.269
57DAP/52DAP	1.14333	0.533
57DAP/7DAP	1.15567	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87609	0.036
17DAP/reference	3.50062	0.006
27DAP/reference	3.60942	0.006
39DAP/reference	4.01533	0.005
41DAP/reference	4.10625	0.011
42DAP/reference	4.45437	0.006
43DAP/reference	5.3236	0.006
47DAP/reference	2.68917	0.133
52DAP/reference	4.11671	0.007
57DAP/reference	3.00537	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3218	0.484
17DAP/reference	0.90799	0.26
27DAP/reference	1.05196	0.81
39DAP/reference	1.00925	1
41DAP/reference	1.00429	0.702
42DAP/reference	0.96525	0.355
43DAP/reference	0.9539	0.43
47DAP/reference	1.05186	0.572
52DAP/reference	0.80473	0.156
57DAP/reference	1.02285	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03531	0.022
17DAP/reference	1.77555	0.467
27DAP/reference	3.11204	0.016
39DAP/reference	2.70501	0.019
41DAP/reference	3.8793	0.006
42DAP/reference	3.13624	0.008
43DAP/reference	2.64995	0.019
47DAP/reference	0.95668	0.452
52DAP/reference	2.4429	0.059
57DAP/reference	1.64807	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98547	1
26DAP/20DAP	1.21867	0.608
34DAP/26DAP	0.83354	0.219
51DAP/34DAP	1.23165	0.108
52DAP/51DAP	0.86089	1
53DAP/52DAP	1.41383	0.047
55DAP/53DAP	0.81884	0.034
57DAP/55DAP	0.95091	0.703
62DAP/57DAP	0.72641	0.003
68DAP/62DAP	0.99981	0.914
68DAP/14DAP	1.17332	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90252	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69034	0.249
Mature Green Tomato/Ripe Tomato	0.63967	0.079
Immature Eggplant/Mature Eggplant	2.03352	0.05
Ripe Pepper/Ripe Tomato	0.77529	1
Mature Eggplant/Ripe Tomato	1.14613	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02585	1
1-1-2/M82	1.05219	1
12-2/M82	1.09774	1
12-4/M82	0.81691	0.358
1-3/M82	1.76049
2-1-1/M82	0.96276
2-1/M82	1.04676	1
2-6/M82	0.58194	1
3-2/M82	1.34752	0.967
4-1-1/M82	0.8124	1
4-1/M82	N/A	N/A
4-3-2/M82	0.73437
4-3/M82	1.617	1
5-3/M82	1.42329	0.572
6-2/M82	1.30028	0.219
6-3/M82	1.03131	1
7-1/M82	0.96889	0.509
7-2/M82	1.11398	1
9-3-2/M82	0.91111

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72622	0.243
IL2-6/WTpooled	1.35075	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77983	0.31
IL12-4/WTpooled	1.02965	1
IL1-4/WTpooled	1.03762
WT/WTpooled	0.96938	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	0.95649	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06784	0.846
DC3000/delta hrp 6h	0.70983	0.95
DC3000/delta hrp 12h	0.80084	1
DC3000/delta hrp 24h	0.89223	0.298

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9704	1
DC3000 delta B/DC3000 delta AB	1.02326	0.761

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84549	1
Exp 36h	0.93779	0.943
Exp 60h	1.36372	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07923	1
Var 0h	3.15237	0.936
Var 12h I row2-row1	1.16629	0.222
Var 12h NI row2-row1	1.09594	0.649
Var 36h I row2-row1	1.14985	1
Var 36h NI row2-row1	1.08837	1
Var 60h I row2-row1	0.78223	0.306
Var 60h NI row2-row1	1.11343	0.904
Time course 0hI-0hNI	0.96849	0.852
Time course 12hI-12hNI	1.15004	0.213
Time course 36hI-36hNI	0.98083	0.46
Time course 60hI-60hNI	0.78449	0.015

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)	1.13165	0.218
transgenic ySAMdc/azygous control (breaker)	0.69577	0.173
transgenic ySAMdc/azygous control (red)	0.88274	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.3379	0.037

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.23489	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88065	1
Manapal/WT (break)	1.22087	0.381
Manapal/WT (red)	0.91477	0.503