Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58681	0.014
27DAP/17DAP	0.58984	0.043
39DAP/27DAP	1.14735	1
41DAP/39DAP	0.71044	0.171
42DAP/41DAP	1.82948	0.059
43DAP/42DAP	2.2075	0.213
47DAP/43DAP	0.5147	0.049
52DAP/47DAP	0.71907	0.294
57DAP/52DAP	1.06945	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.03163	0.006
17DAP/reference	1.85687	0.028
27DAP/reference	1.95469	0.011
39DAP/reference	0.86374	0.261
41DAP/reference	0.83542	0.114
42DAP/reference	0.83674	0.015
43DAP/reference	0.64817	0.013
47DAP/reference	0.53837	0.001
52DAP/reference	0.76094	0.021
57DAP/reference	0.82846	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92279	0.56
27DAP/17DAP	0.92199	0.684
39DAP/27DAP	0.61703	0.044
41DAP/39DAP	0.30409	0.013
42DAP/41DAP	1.02209	0.892
43DAP/42DAP	3.03666	0.013
47DAP/43DAP	0.59037	0.009
52DAP/47DAP	1.49881	0.343
57DAP/52DAP	1.10985	0.763
57DAP/7DAP	0.48418	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.29288	0.024
17DAP/reference	1.28557	0.028
27DAP/reference	1.04484	0.664
39DAP/reference	0.9653	0.307
41DAP/reference	0.79094	0.04
42DAP/reference	1.17491	0.1
43DAP/reference	0.95258	0.403
47DAP/reference	0.65945	0.038
52DAP/reference	0.92527	0.254
57DAP/reference	0.89569	0.057

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86042	0.069
17DAP/reference	2.2433	0.007
27DAP/reference	1.59812	0.029
39DAP/reference	0.58031	0.012
41DAP/reference	1.01793	0.649
42DAP/reference	1.65528	0.013
43DAP/reference	0.78592	0.066
47DAP/reference	0.86769	0.133
52DAP/reference	0.47003	0.003
57DAP/reference	0.37695	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.67925	0.015
17DAP/reference	1.7677	0.095
27DAP/reference	1.59716	0.019
39DAP/reference	1.07408	0.189
41DAP/reference	1.12221	0.257
42DAP/reference	0.89561	0.172
43DAP/reference	0.81326	0.047
47DAP/reference	0.43059	0.004
52DAP/reference	0.49044	0.097
57DAP/reference	0.6113	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96913	1
26DAP/20DAP	0.99813	1
34DAP/26DAP	1.16272	1
51DAP/34DAP	0.61078	0.07
52DAP/51DAP	1.12832	0.261
53DAP/52DAP	0.64105	0.052
55DAP/53DAP	0.52398	0.029
57DAP/55DAP	0.90923	0.677
62DAP/57DAP	1.3024	0.002
68DAP/62DAP	0.68785	0.378
68DAP/14DAP	0.23454	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.43153	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.98593	0.058
Mature Green Tomato/Ripe Tomato	2.89143	0.02
Immature Eggplant/Mature Eggplant	0.31194	0.057
Ripe Pepper/Ripe Tomato	30.9029	0.258
Mature Eggplant/Ripe Tomato	43.3931	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.76491
12-2/M82	N/A	N/A
12-4/M82	1.22923	1
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	2.31898
4-3-2/M82	0.68396
4-3/M82	N/A	N/A
5-3/M82	1.07412	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	1.66563
9-3-2/M82	1.4397

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99579	1
IL2-6/WTpooled	1.14046	0.419
IL7-5/WTpooled	0.68616	1
IL7-3/WTpooled	0.87628	0.418
IL12-4/WTpooled	1.0209	0.839
IL1-4/WTpooled	0.88682	0.562
WT/WTpooled	0.98695	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	1.14144	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97371	1
DC3000/delta hrp 6h	0.91437	0.95
DC3000/delta hrp 12h	1.1147	1
DC3000/delta hrp 24h	0.45412	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.51945	0.024
DC3000 delta B/DC3000 delta AB	0.59209	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03493	1
Exp 36h	0.83136	0.504
Exp 60h	0.85158	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02611	1
Var 0h	1.30321	0.259
Var 12h I row2-row1	0.95921	0.856
Var 12h NI row2-row1	0.92139	0.906
Var 36h I row2-row1	0.90745	1
Var 36h NI row2-row1	1.14657	1
Var 60h I row2-row1	0.88466	0.832
Var 60h NI row2-row1	1.05646	1
Time course 0hI-0hNI	1.09388	0.662
Time course 12hI-12hNI	0.98312	0.909
Time course 36hI-36hNI	0.91129	0.096
Time course 60hI-60hNI	0.28012	0.006

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)	1.06165	0.798
transgenic ySAMdc/azygous control (breaker)	1.71773	1
transgenic ySAMdc/azygous control (red)	1.50525	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.75397	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.25925	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05267	0.307
Manapal/WT (break)	1.99604	0.381
Manapal/WT (red)	2.58172	0.222