Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14093	0.63
27DAP/17DAP	1.00881	1
39DAP/27DAP	1.58034	0.188
41DAP/39DAP	0.89954	0.582
42DAP/41DAP	1.31301	0.767
43DAP/42DAP	1.36079	0.968
47DAP/43DAP	0.61205	0.079
52DAP/47DAP	0.93913	0.803
57DAP/52DAP	1.33955	0.883

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.189	0.241
17DAP/reference	1.19518	0.442
27DAP/reference	0.99573	0.779
39DAP/reference	1.42307	0.486
41DAP/reference	1.19212	0.145
42DAP/reference	3.20026	0.001
43DAP/reference	1.92133	0.007
47DAP/reference	1.66105	0.001
52DAP/reference	1.09061	0.8
57DAP/reference	1.32133	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17755	0.348
27DAP/17DAP	0.98669	0.943
39DAP/27DAP	1.12799	0.685
41DAP/39DAP	1.06277	1
42DAP/41DAP	1.20134	0.783
43DAP/42DAP	1.15758	0.627
47DAP/43DAP	0.94867	0.823
52DAP/47DAP	0.94285	0.884
57DAP/52DAP	0.87917	0.436
57DAP/7DAP	0.80277	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16426	0.157
17DAP/reference	1.083	0.627
27DAP/reference	0.97095	0.656
39DAP/reference	1.57188	0.017
41DAP/reference	1.27043	0.177
42DAP/reference	1.2099	0.405
43DAP/reference	1.32019	0.026
47DAP/reference	3.23074	0.018
52DAP/reference	1.1011	0.328
57DAP/reference	1.52772	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87814	0.296
17DAP/reference	1.57559	0.053
27DAP/reference	1.34349	0.235
39DAP/reference	1.85228	0.031
41DAP/reference	1.1222	0.459
42DAP/reference	1.42083	0.011
43DAP/reference	1.25104	0.728
47DAP/reference	1.64367	0.076
52DAP/reference	1.24758	0.011
57DAP/reference	1.23028	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84822	0.158
17DAP/reference	1.25038	0.306
27DAP/reference	1.08522	0.575
39DAP/reference	1.10224	0.578
41DAP/reference	1.01342	0.754
42DAP/reference	1.29263	0.4
43DAP/reference	2.32563	0.175
47DAP/reference	1.24734	0.251
52DAP/reference	1.02339	0.888
57DAP/reference	2.20145	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06872	0.966
26DAP/20DAP	1.69641	0.273
34DAP/26DAP	0.80047	0.228
51DAP/34DAP	1.32716	0.103
52DAP/51DAP	0.86661	1
53DAP/52DAP	0.93673	0.535
55DAP/53DAP	0.54242	0.016
57DAP/55DAP	0.86786	0.486
62DAP/57DAP	2.96882	0.018
68DAP/62DAP	0.69607	0.7
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.01602	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.51281	0.075
Mature Green Tomato/Ripe Tomato	1.20149	0.948
Immature Eggplant/Mature Eggplant	0.6977	0.096
Ripe Pepper/Ripe Tomato	0.50122	0.224
Mature Eggplant/Ripe Tomato	0.52352	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92628	0.907
1-1-2/M82	1.41396	1
12-2/M82	1.17133	1
12-4/M82	1.50772	1
1-3/M82	1.33172	0.479
2-1-1/M82	1.08097	0.764
2-1/M82	0.58073	0.325
2-6/M82	1.03832	0.695
3-2/M82	0.95663	0.752
4-1-1/M82	1.30119	1
4-1/M82	2.04531	0.853
4-3-2/M82	1.74421	0.241
4-3/M82	1.20593	1
5-3/M82	0.92638	1
6-2/M82	1.71233	1
6-3/M82	1.13336	1
7-1/M82	1.06902	0.598
7-2/M82	1.44537	0.385
9-3-2/M82	1.57995	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.70298
IL2-6/WTpooled	1.32977	1
IL7-5/WTpooled	0.49008
IL7-3/WTpooled	1.14433	1
IL12-4/WTpooled	1.02575
IL1-4/WTpooled	1.22337	1
WT/WTpooled	0.94696	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	0.91647	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03263	0.921
DC3000/delta hrp 6h	1.00218	0.95
DC3000/delta hrp 12h	1.12568	1
DC3000/delta hrp 24h	0.81114	0.1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50728	0.025
DC3000 delta B/DC3000 delta AB	0.46502	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82957	1
Exp 36h	1.71711	1
Exp 60h	0.80776	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03803	1
Var 0h	1.28162	0.782
Var 12h I row2-row1	0.98345	1
Var 12h NI row2-row1	0.99318	1
Var 36h I row2-row1	1.0025	1
Var 36h NI row2-row1	0.91089	0.421
Var 60h I row2-row1	0.79306	0.293
Var 60h NI row2-row1	0.97178	1
Time course 0hI-0hNI	0.98931	1
Time course 12hI-12hNI	1.01116	0.836
Time course 36hI-36hNI	0.96106	0.255
Time course 60hI-60hNI	0.54145	0.009

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)	1.07237	0.541
transgenic ySAMdc/azygous control (breaker)	0.59363	0.139
transgenic ySAMdc/azygous control (red)	0.86723	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08253	0.063

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56548	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.02633	1
Manapal/WT (break)	0.91782	0.333
Manapal/WT (red)	0.97835	0.863