Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.6.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.56061	0.325
27DAP/17DAP	0.80471	0.539
39DAP/27DAP	0.84352	0.435
41DAP/39DAP	1.32416	0.342
42DAP/41DAP	1.93741	0.404
43DAP/42DAP	0.99257	0.937
47DAP/43DAP	1.22437	0.842
52DAP/47DAP	0.8137	0.503
57DAP/52DAP	1.32936	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89004	0.2
17DAP/reference	0.94956	0.474
27DAP/reference	1.06843	0.548
39DAP/reference	1.04782	0.628
41DAP/reference	0.9193	0.267
42DAP/reference	0.97425	0.326
43DAP/reference	1.05749	0.705
47DAP/reference	1.25946	0.005
52DAP/reference	1.27409	0.01
57DAP/reference	1.25312	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3585	0.473
27DAP/17DAP	1.11063	0.96
39DAP/27DAP	0.91337	0.52
41DAP/39DAP	0.91817	0.764
42DAP/41DAP	1.18599	0.559
43DAP/42DAP	0.89512	0.415
47DAP/43DAP	0.88473	0.325
52DAP/47DAP	0.97766	0.902
57DAP/52DAP	0.93566	0.608
57DAP/7DAP	1.64749	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87467	0.108
17DAP/reference	1.15075	0.269
27DAP/reference	1.06455	0.664
39DAP/reference	1.5939	0.007
41DAP/reference	1.81051	0.014
42DAP/reference	1.46336	0.014
43DAP/reference	1.19861	0.132
47DAP/reference	0.99615	1
52DAP/reference	1.2515	0.832
57DAP/reference	1.28308	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00993	0.951
17DAP/reference	1.036	1
27DAP/reference	1.2632	0.1
39DAP/reference	1.10183	0.764
41DAP/reference	0.93813	0.331
42DAP/reference	1.09205	0.195
43DAP/reference	1.0863	0.874
47DAP/reference	1.03295	0.544
52DAP/reference	1.08717	0.444
57DAP/reference	0.88747	0.243

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94193	0.311
17DAP/reference	1.05077	0.62
27DAP/reference	1.20173	0.059
39DAP/reference	1.02662	0.858
41DAP/reference	1.04249	0.916
42DAP/reference	0.95403	0.552
43DAP/reference	1.0951	0.375
47DAP/reference	1.06299	0.934
52DAP/reference	0.99311	0.821
57DAP/reference	1.44535	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92233	0.773
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.36823	0.819
51DAP/34DAP	1.26192	0.473
52DAP/51DAP	1.00794	1
53DAP/52DAP	1.38324	0.517
55DAP/53DAP	1.40842	0.477
57DAP/55DAP	1.66069	0.348
62DAP/57DAP	0.80187	0.162
68DAP/62DAP	1.41404	0.162
68DAP/14DAP	0.90717	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.35616	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.21051	0.089
Mature Green Tomato/Ripe Tomato	1.50344	0.016
Immature Eggplant/Mature Eggplant	2.0018	0.05
Ripe Pepper/Ripe Tomato	0.33768	0.293
Mature Eggplant/Ripe Tomato	0.42782	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07924	1
1-1-2/M82	1.21248	1
12-2/M82	1.38632
12-4/M82	1.23368	0.611
1-3/M82	0.85264	1
2-1-1/M82	1.08834
2-1/M82	N/A	N/A
2-6/M82	0.82817	0.501
3-2/M82	0.80961
4-1-1/M82	0.79703	1
4-1/M82	2.02969
4-3-2/M82	N/A	N/A
4-3/M82	0.83017
5-3/M82	0.96365	1
6-2/M82	0.50109
6-3/M82	0.98203	1
7-1/M82	1.01579	1
7-2/M82	0.72217	0.796
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.01161	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13476	1
IL12-4/WTpooled	0.99574	1
IL1-4/WTpooled	0.88418
WT/WTpooled	0.97329	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	0.87761	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96888	1
DC3000/delta hrp 6h	1.11974	1
DC3000/delta hrp 12h	0.93212	1
DC3000/delta hrp 24h	1.02169	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2073	0.313
DC3000 delta B/DC3000 delta AB	0.91903	0.638

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03043	1
Exp 36h	1.09596	0.693
Exp 60h	1.21093	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02156	1
Var 0h	0.72151	1
Var 12h I row2-row1	0.87766	0.338
Var 12h NI row2-row1	0.94929	0.82
Var 36h I row2-row1	1.04174	1
Var 36h NI row2-row1	1.12279	1
Var 60h I row2-row1	0.98563	1
Var 60h NI row2-row1	0.98828	1
Time course 0hI-0hNI	0.97203	0.858
Time course 12hI-12hNI	0.99352	1
Time course 36hI-36hNI	0.88863	0.144
Time course 60hI-60hNI	0.27733	0.005

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)	1.04596	0.748
transgenic ySAMdc/azygous control (breaker)	0.97464	1
transgenic ySAMdc/azygous control (red)	0.978	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97235	0.172

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.92966	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90079	1
Manapal/WT (break)	0.89056	1
Manapal/WT (red)	1.27394	0.137