Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.3.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76953	0.19
27DAP/17DAP	1.00863	1
39DAP/27DAP	1.66785	0.677
41DAP/39DAP	0.97252	0.897
42DAP/41DAP	0.93729	1
43DAP/42DAP	1.30907	0.619
47DAP/43DAP	0.91035	0.671
52DAP/47DAP	0.90281	0.709
57DAP/52DAP	0.98388	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14765	0.567
17DAP/reference	0.92854	0.24
27DAP/reference	1.08778	0.696
39DAP/reference	0.90963	0.097
41DAP/reference	0.9165	0.434
42DAP/reference	0.82297	0.035
43DAP/reference	0.95471	0.675
47DAP/reference	1.05824	0.862
52DAP/reference	1.77629	0.335
57DAP/reference	1.35577	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81252	0.194
27DAP/17DAP	1.29186	0.653
39DAP/27DAP	0.7996	0.338
41DAP/39DAP	1.14364	0.774
42DAP/41DAP	0.77438	0.069
43DAP/42DAP	1.14539	0.25
47DAP/43DAP	0.9962	0.99
52DAP/47DAP	1.11218	0.982
57DAP/52DAP	0.82212	0.422
57DAP/7DAP	1.30563	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38944	0.042
17DAP/reference	1.37173	0.014
27DAP/reference	1.28183	0.06
39DAP/reference	1.48073	0.006
41DAP/reference	1.29174	0.066
42DAP/reference	1.33164	0.059
43DAP/reference	1.19889	0.364
47DAP/reference	1.11997	0.395
52DAP/reference	1.20481	0.048
57DAP/reference	1.45473	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97607	0.706
17DAP/reference	0.98622	0.693
27DAP/reference	0.85284	0.173
39DAP/reference	0.8894	0.227
41DAP/reference	0.92078	0.277
42DAP/reference	0.86972	0.237
43DAP/reference	0.84927	0.098
47DAP/reference	0.88915	0.04
52DAP/reference	0.88952	0.131
57DAP/reference	0.82417	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32773	0.153
17DAP/reference	1.16691	0.699
27DAP/reference	1.59563	0.017
39DAP/reference	1.38251	0.019
41DAP/reference	1.32846	0.072
42DAP/reference	1.39235	0.108
43DAP/reference	1.00466	0.767
47DAP/reference	1.16807	0.022
52DAP/reference	1.35048	0.186
57DAP/reference	0.95154	0.41

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97142	1
26DAP/20DAP	0.96552	1
34DAP/26DAP	1.02904	1
51DAP/34DAP	1.2931	0.059
52DAP/51DAP	0.87689	1
53DAP/52DAP	0.92827	0.715
55DAP/53DAP	0.84986	0.5
57DAP/55DAP	0.93861	0.78
62DAP/57DAP	1.21542
68DAP/62DAP	1.04709	1
68DAP/14DAP	0.8595	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.4164	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.3672	0.113
Mature Green Tomato/Ripe Tomato	1.01342	0.898
Immature Eggplant/Mature Eggplant	0.82665	0.254
Ripe Pepper/Ripe Tomato	2.17138	0.258
Mature Eggplant/Ripe Tomato	1.40618	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.70673
12-2/M82	0.8413
12-4/M82	0.78162	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.95733	1
2-1/M82	0.91645
2-6/M82	N/A	N/A
3-2/M82	1.25106
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.24439	1
5-3/M82	1.13037	1
6-2/M82	1.07488	1
6-3/M82	1.01115
7-1/M82	1.267
7-2/M82	1.44841
9-3-2/M82	1.54591

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83542	0.247
IL2-6/WTpooled	1.06075	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.1109	1
IL12-4/WTpooled	1.12282	0.557
IL1-4/WTpooled	0.88069	0.415
WT/WTpooled	1.00395	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	0.86525	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92781	0.868
DC3000/delta hrp 6h	1.18763	1
DC3000/delta hrp 12h	0.9165	1
DC3000/delta hrp 24h	0.44987	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.41874	0.024
DC3000 delta B/DC3000 delta AB	0.59096	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.77692	1
Exp 36h	0.85617	0.699
Exp 60h	0.72181	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04379	1
Var 0h	0.8288	0.457
Var 12h I row2-row1	1.09196	0.506
Var 12h NI row2-row1	1.20288	0.649
Var 36h I row2-row1	0.82093	0.805
Var 36h NI row2-row1	1.07957	1
Var 60h I row2-row1	0.97711
Var 60h NI row2-row1	1.54849	0.691
Time course 0hI-0hNI	0.99449	1
Time course 12hI-12hNI	0.89802	0.292
Time course 36hI-36hNI	0.82461	0.028
Time course 60hI-60hNI	0.26704	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)	0.84916	0.391
transgenic ySAMdc/azygous control (breaker)	0.81892	0.251
transgenic ySAMdc/azygous control (red)	1.55366	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11099	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.37707	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.24388	0.086
Manapal/WT (break)	0.83387	0.333
Manapal/WT (red)	1.32631	0.413