Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.19.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.79931	0.2
27DAP/17DAP	0.65861	0.046
39DAP/27DAP	0.90952	0.631
41DAP/39DAP	1.17866	0.603
42DAP/41DAP	1.53654	0.899
43DAP/42DAP	1.43561	0.974
47DAP/43DAP	1.46693	0.793
52DAP/47DAP	0.81224	0.539
57DAP/52DAP	1.1394	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41993	0.031
17DAP/reference	1.50701	0.083
27DAP/reference	1.17806	0.339
39DAP/reference	1.36524	0.027
41DAP/reference	1.58305	0.03
42DAP/reference	1.19991	0.022
43DAP/reference	1.18146	0.126
47DAP/reference	1.14715	0.096
52DAP/reference	1.37141	0.048
57DAP/reference	1.18963	0.043

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14715	0.138
27DAP/17DAP	0.85968	0.537
39DAP/27DAP	0.74084	0.126
41DAP/39DAP	1.07011	0.909
42DAP/41DAP	1.36795	0.003
43DAP/42DAP	0.72561	0.028
47DAP/43DAP	0.86841	0.41
52DAP/47DAP	2.68456	0.048
57DAP/52DAP	3.13303	0.033
57DAP/7DAP	2.24845	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00883	1
17DAP/reference	0.92693	0.253
27DAP/reference	0.8395	0.019
39DAP/reference	0.86687	0.264
41DAP/reference	1.01149	0.677
42DAP/reference	1.0563	0.675
43DAP/reference	0.98873	0.637
47DAP/reference	0.86475	0.293
52DAP/reference	0.83426	0.213
57DAP/reference	0.92742	0.24

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22935	0.491
17DAP/reference	1.13037	0.531
27DAP/reference	1.04785	0.847
39DAP/reference	1.19725	0.316
41DAP/reference	1.24985	0.03
42DAP/reference	1.09384	0.408
43DAP/reference	0.84911	0.157
47DAP/reference	1.33969	0.038
52DAP/reference	1.17549	0.208
57DAP/reference	1.06133	0.908

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92671	0.29
17DAP/reference	0.98208	0.668
27DAP/reference	1.01713	1
39DAP/reference	0.98447	0.591
41DAP/reference	0.97912	0.618
42DAP/reference	1.04188	0.789
43DAP/reference	0.88699	0.246
47DAP/reference	1.29748	0.424
52DAP/reference	0.90476	0.444
57DAP/reference	1.11361	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99124	1
26DAP/20DAP	1.66673	1
34DAP/26DAP	4.37394	0.819
51DAP/34DAP	1.6947	0.967
52DAP/51DAP	6.14059	0.033
53DAP/52DAP	0.60412	0.049
55DAP/53DAP	1.67747	0.047
57DAP/55DAP	0.5026	0.033
62DAP/57DAP	1.757	0.515
68DAP/62DAP	4.01511	0.747
68DAP/14DAP	0.83152

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.10464	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.40641
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.83704
Mature Eggplant/Ripe Tomato	0.62837	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.20385
12-2/M82	N/A	N/A
12-4/M82	0.9526	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.95202
2-1/M82	N/A	N/A
2-6/M82	0.8296	1
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	1.06614	1
6-2/M82	N/A	N/A
6-3/M82	0.86449
7-1/M82	N/A	N/A
7-2/M82	0.76903	0.553
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.63145	0.277
IL2-6/WTpooled	0.56385	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.32936	0.362
IL12-4/WTpooled	1.21487	0.646
IL1-4/WTpooled	0.877	0.562
WT/WTpooled	0.9813	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	0.89468	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91823	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.7988	1
DC3000/delta hrp 24h	1.00177	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.36063	0.042
DC3000 delta B/DC3000 delta AB	1.43175	0.129

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01328	1
Var 0h	0.92482	0.933
Var 12h I row2-row1	0.70574	0.467
Var 12h NI row2-row1	1.14644	0.649
Var 36h I row2-row1	1.08629	1
Var 36h NI row2-row1	1.48237	0.253
Var 60h I row2-row1	0.79574	0.306
Var 60h NI row2-row1	0.94925	1
Time course 0hI-0hNI	0.92229	0.59
Time course 12hI-12hNI	1.02448	0.956
Time course 36hI-36hNI	0.84264	0.194
Time course 60hI-60hNI	0.45808	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)	1.80983	0.921
transgenic ySAMdc/azygous control (breaker)	1.21364	1
transgenic ySAMdc/azygous control (red)	0.68778	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90606	0.089

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10704	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.40976	0.222