Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1916	0.77
27DAP/17DAP	0.67555	0.149
39DAP/27DAP	2.52862	0.038
41DAP/39DAP	1.3342	0.255
42DAP/41DAP	2.6176	0.026
43DAP/42DAP	1.97878	0.799
47DAP/43DAP	1.07205	0.959
52DAP/47DAP	0.51729	0.067
57DAP/52DAP	1.36292	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.36483	0.024
17DAP/reference	0.51721	0.007
27DAP/reference	0.65417	0.015
39DAP/reference	1.30727	0.747
41DAP/reference	0.86796	0.201
42DAP/reference	3.49415	0.001
43DAP/reference	3.51432	0.006
47DAP/reference	2.70368	0.001
52DAP/reference	1.3995	0.012
57DAP/reference	2.3927	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99295	0.782
27DAP/17DAP	0.8313	0.475
39DAP/27DAP	0.84489	0.382
41DAP/39DAP	1.4576	0.735
42DAP/41DAP	0.98712	0.774
43DAP/42DAP	0.81201	0.076
47DAP/43DAP	0.96372	0.823
52DAP/47DAP	1.15353	0.609
57DAP/52DAP	0.90585	0.584
57DAP/7DAP	0.38814	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97952	0.55
17DAP/reference	0.83727	0.295
27DAP/reference	0.86301	0.066
39DAP/reference	0.93329	0.23
41DAP/reference	1.01392	0.741
42DAP/reference	0.69779	0.021
43DAP/reference	0.9863	0.58
47DAP/reference	1.95376	0.018
52DAP/reference	1.09929	0.563
57DAP/reference	0.89464	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.29567	0.005
17DAP/reference	0.31599	0.003
27DAP/reference	0.39214	0.005
39DAP/reference	0.3551	0.009
41DAP/reference	0.74488	0.064
42DAP/reference	0.53327	0.011
43DAP/reference	0.58634	0.02
47DAP/reference	0.68816	0.014
52DAP/reference	0.42698	0.007
57DAP/reference	0.4216	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86085	0.391
17DAP/reference	0.6095	0.203
27DAP/reference	0.41695
39DAP/reference	0.62684	0.147
41DAP/reference	1.00203	0.826
42DAP/reference	2.41436	0.074
43DAP/reference	4.03252	0.021
47DAP/reference	3.2863	0.005
52DAP/reference	2.03829	0.233
57DAP/reference	1.55705	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94152	1
26DAP/20DAP	1.37848	0.273
34DAP/26DAP	1.05403	1
51DAP/34DAP	0.96877	0.779
52DAP/51DAP	0.78948	1
53DAP/52DAP	1.22404	0.179
55DAP/53DAP	0.70434	0.043
57DAP/55DAP	1.58049	0.049
62DAP/57DAP	1.03171	0.994
68DAP/62DAP	0.93604	0.722
68DAP/14DAP	9.34521	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.63989	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.14763	0.055
Mature Green Tomato/Ripe Tomato	0.62484	0.096
Immature Eggplant/Mature Eggplant	2.10315	0.05
Ripe Pepper/Ripe Tomato	1.07944	1
Mature Eggplant/Ripe Tomato	0.76195	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18283	0.877
1-1-2/M82	1.4148	0.977
12-2/M82	1.25396	0.125
12-4/M82	1.36401	1
1-3/M82	0.72001
2-1-1/M82	1.0135	1
2-1/M82	0.48296
2-6/M82	0.85885	0.501
3-2/M82	1.06131	0.84
4-1-1/M82	0.61152
4-1/M82	1.14677	1
4-3-2/M82	1.30644	1
4-3/M82	1.39205
5-3/M82	1.94459	0.37
6-2/M82	1.04243
6-3/M82	0.76152	1
7-1/M82	0.88109
7-2/M82	0.98971	0.881
9-3-2/M82	0.79701	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.27115	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87841	0.418
IL12-4/WTpooled	0.74544	0.554
IL1-4/WTpooled	0.91595	0.834
WT/WTpooled	1.07942	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	1.07721	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99525	1
DC3000/delta hrp 6h	0.83253	0.95
DC3000/delta hrp 12h	1.06593	1
DC3000/delta hrp 24h	0.64055	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67569	0.027
DC3000 delta B/DC3000 delta AB	0.6993	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13811	1
Exp 36h	1.19654	0.489
Exp 60h	1.37287	0.227

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04285	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.26578	0.473
Var 12h NI row2-row1	1.04667	1
Var 36h I row2-row1	1.07473	0.908
Var 36h NI row2-row1	1.2102	0.482
Var 60h I row2-row1	0.85875	0.293
Var 60h NI row2-row1	1.03861	1
Time course 0hI-0hNI	1.00497	1
Time course 12hI-12hNI	1.14595	0.109
Time course 36hI-36hNI	1.21374	0.005
Time course 60hI-60hNI	1.04276	1

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)	0.46151	0.246
transgenic ySAMdc/azygous control (breaker)	0.97995	1
transgenic ySAMdc/azygous control (red)	0.98947	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.17119	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40612	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.23258	0.14
Manapal/WT (break)	1.19327	0.381
Manapal/WT (red)	0.7437	0.274