Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.16.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23784	0.325
27DAP/17DAP	0.47493	0.032
39DAP/27DAP	0.73857	0.425
41DAP/39DAP	0.71649	0.109
42DAP/41DAP	0.85145	1
43DAP/42DAP	1.10925	1
47DAP/43DAP	0.54668	0.057
52DAP/47DAP	1.07653	0.934
57DAP/52DAP	0.87383	0.895

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7844	0.063
17DAP/reference	0.63525	0.012
27DAP/reference	0.60088	0.018
39DAP/reference	0.64481	0.022
41DAP/reference	0.55315	0.01
42DAP/reference	0.5805	0.001
43DAP/reference	0.69616	0.103
47DAP/reference	0.56532	0.001
52DAP/reference	0.49093	0.018
57DAP/reference	0.66971	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82021	0.036
27DAP/17DAP	0.72561	0.195
39DAP/27DAP	0.32178	0.028
41DAP/39DAP	1.41402	0.091
42DAP/41DAP	0.8374	0.093
43DAP/42DAP	0.61618	0.027
47DAP/43DAP	0.96677	0.857
52DAP/47DAP	0.67202	0.105
57DAP/52DAP	0.89662	0.56
57DAP/7DAP	0.57528	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07847	0.534
17DAP/reference	0.75129	0.013
27DAP/reference	0.54613	0.01
39DAP/reference	0.39393	0.011
41DAP/reference	0.37126	0.009
42DAP/reference	0.29673	0.01
43DAP/reference	0.25686	0.008
47DAP/reference	0.36814	0.03
52DAP/reference	0.35135	0.01
57DAP/reference	0.29843	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.57325	0.008
17DAP/reference	0.64913	0.033
27DAP/reference	0.64048	0.02
39DAP/reference	0.46317	0.008
41DAP/reference	0.61984	0.009
42DAP/reference	0.58624	0.013
43DAP/reference	0.38295	0.003
47DAP/reference	0.65499	0.007
52DAP/reference	0.38438	0.003
57DAP/reference	0.32539	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.87255	0.02
17DAP/reference	1.77215	0.135
27DAP/reference	1.34522	0.059
39DAP/reference	0.94955	0.328
41DAP/reference	0.67067	0.022
42DAP/reference	0.52305	0.019
43DAP/reference	0.51425	0.018
47DAP/reference	0.46112	0.004
52DAP/reference	0.33315	0.043
57DAP/reference	0.90669	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.92888	1
26DAP/20DAP	0.97389	1
34DAP/26DAP	0.93329	0.848
51DAP/34DAP	0.41399	0.049
52DAP/51DAP	0.97687	1
53DAP/52DAP	0.60565	0.049
55DAP/53DAP	0.723	0.154
57DAP/55DAP	1.25798	0.728
62DAP/57DAP	0.99996	0.994
68DAP/62DAP	1.02115	0.885
68DAP/14DAP	0.6688	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51155	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.39582	0.058
Mature Green Tomato/Ripe Tomato	5.02975	0.015
Immature Eggplant/Mature Eggplant	0.53949	0.057
Ripe Pepper/Ripe Tomato	2.47232	1
Mature Eggplant/Ripe Tomato	4.14495	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80363	0.605
1-1-2/M82	0.94094	0.958
12-2/M82	0.69973	0.74
12-4/M82	0.73652
1-3/M82	1.56965
2-1-1/M82	1.23128
2-1/M82	1.37624	0.335
2-6/M82	N/A	N/A
3-2/M82	1.08323	0.717
4-1-1/M82	1.33014	0.968
4-1/M82	N/A	N/A
4-3-2/M82	1.36038	0.284
4-3/M82	1.02553	1
5-3/M82	1.52406	1
6-2/M82	1.35531	1
6-3/M82	0.98377	1
7-1/M82	1.12411	0.992
7-2/M82	1.29676	0.318
9-3-2/M82	1.13047	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.02194	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94783	1
DC3000/delta hrp 6h	0.91442	0.95
DC3000/delta hrp 12h	1.16656	1
DC3000/delta hrp 24h	1.06543	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9432	0.413
DC3000 delta B/DC3000 delta AB	0.54896	0.025

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01132	1
Exp 36h	0.88166	0.589
Exp 60h	0.85889	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97573	1
Var 0h	0.86713	0.933
Var 12h I row2-row1	0.98827	1
Var 12h NI row2-row1	1.03606	0.649
Var 36h I row2-row1	0.87144	1
Var 36h NI row2-row1	1.10587	0.482
Var 60h I row2-row1	1.33303	0.562
Var 60h NI row2-row1	1.05836	0.904
Time course 0hI-0hNI	1.01081	1
Time course 12hI-12hNI	1.0406	0.756
Time course 36hI-36hNI	0.98435	0.569
Time course 60hI-60hNI	0.72182	0.161

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)	1.01604	0.748
transgenic ySAMdc/azygous control (breaker)	1.54352	0.162
transgenic ySAMdc/azygous control (red)	1.04236	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.59539	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.56316	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.29975	0.09
Manapal/WT (break)	2.1852	0.13
Manapal/WT (red)	1.18565	0.413