Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.7.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19864	0.512
27DAP/17DAP	1.12754	0.849
39DAP/27DAP	1.01053	0.82
41DAP/39DAP	1.25786	0.691
42DAP/41DAP	2.76075	0.063
43DAP/42DAP	1.83527	0.106
47DAP/43DAP	0.68064	0.168
52DAP/47DAP	0.57335	0.071
57DAP/52DAP	0.98236	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95197	0.412
17DAP/reference	1.10523	0.051
27DAP/reference	1.00749	1
39DAP/reference	1.04867	0.413
41DAP/reference	0.99374	1
42DAP/reference	0.87035	0.012
43DAP/reference	0.97112	0.631
47DAP/reference	0.91197	0.127
52DAP/reference	0.92971	0.215
57DAP/reference	0.98629	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.21713	0.736
27DAP/17DAP	1.19841	1
39DAP/27DAP	1.27193	1
41DAP/39DAP	1.15752	0.868
42DAP/41DAP	0.99617	0.83
43DAP/42DAP	1.242	0.162
47DAP/43DAP	0.77363	0.476
52DAP/47DAP	0.76663	0.498
57DAP/52DAP	0.96542	0.784
57DAP/7DAP	1.26884	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87039	0.246
17DAP/reference	0.78598	0.064
27DAP/reference	0.70077	0.01
39DAP/reference	0.87475	0.043
41DAP/reference	0.97922	0.589
42DAP/reference	0.95389	0.355
43DAP/reference	0.84955	0.21
47DAP/reference	0.96899	0.671
52DAP/reference	0.94694	0.363
57DAP/reference	0.76543	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90333	0.342
17DAP/reference	0.83759	0.009
27DAP/reference	1.0641	0.933
39DAP/reference	1.02792	1
41DAP/reference	0.96286	0.422
42DAP/reference	0.97408	0.482
43DAP/reference	1.00163	0.761
47DAP/reference	0.9505	0.302
52DAP/reference	1.06012	0.789
57DAP/reference	1.0491	0.887

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7739	0.071
17DAP/reference	0.8938	0.255
27DAP/reference	0.74158	0.042
39DAP/reference	0.8123	0.058
41DAP/reference	0.77079	0.022
42DAP/reference	1.54933	0.017
43DAP/reference	1.55264	0.205
47DAP/reference	0.95052	0.383
52DAP/reference	0.75941	0.186
57DAP/reference	0.78754	0.055

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16412	0.966
26DAP/20DAP	0.95693	1
34DAP/26DAP	1.42872	1
51DAP/34DAP	1.13808	0.785
52DAP/51DAP	1.23285	0.596
53DAP/52DAP	1.0212	0.983
55DAP/53DAP	1.6057	0.771
57DAP/55DAP	1.49913	0.694
62DAP/57DAP	1.04303	1
68DAP/62DAP	1.3104	0.626
68DAP/14DAP	1.55371	0.211

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.68648	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.95651	0.611
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.29903	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.7052
12-2/M82	N/A	N/A
12-4/M82	3.47243
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	1.76717
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	0.72513	1
6-2/M82	13.1857
6-3/M82	N/A	N/A
7-1/M82	0.86743
7-2/M82	N/A	N/A
9-3-2/M82	1.44409

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.84179	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.30531	0.362
IL12-4/WTpooled	1.0458	0.785
IL1-4/WTpooled	0.74539	0.834
WT/WTpooled	1.0198	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	1.08748	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91073	1
DC3000/delta hrp 6h	0.92496	0.95
DC3000/delta hrp 12h	0.97574	1
DC3000/delta hrp 24h	0.68666	0.04

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.09918	1
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	1.01184	1
Var 0h	1.04667	1
Var 12h I row2-row1	1.31417	0.613
Var 12h NI row2-row1	1.00954	0.649
Var 36h I row2-row1	0.66415	0.202
Var 36h NI row2-row1	1.09491	1
Var 60h I row2-row1	1.24738	0.543
Var 60h NI row2-row1	1.0935	1
Time course 0hI-0hNI	0.8671	0.287
Time course 12hI-12hNI	0.79256	0.055
Time course 36hI-36hNI	0.81093	0.159
Time course 60hI-60hNI	0.2889	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)	0.91801	0.338
transgenic ySAMdc/azygous control (breaker)	1.08959	0.248
transgenic ySAMdc/azygous control (red)	1.12861	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9797	0.295

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07235	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18	0.14
Manapal/WT (break)	0.88072	1
Manapal/WT (red)	1.57032	0.413