Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22447	0.561
27DAP/17DAP	1.10885	0.902
39DAP/27DAP	1.12397	1
41DAP/39DAP	0.86896	0.485
42DAP/41DAP	1.48232	0.691
43DAP/42DAP	0.99716	0.937
47DAP/43DAP	0.99121	0.895
52DAP/47DAP	1.59373	0.61
57DAP/52DAP	1.52523	0.44

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27601	0.045
17DAP/reference	1.2332	0.33
27DAP/reference	1.18676	0.221
39DAP/reference	1.04561	0.691
41DAP/reference	1.24763	0.062
42DAP/reference	1.06088	0.467
43DAP/reference	0.84652	0.071
47DAP/reference	0.98309	0.535
52DAP/reference	1.20893	0.335
57DAP/reference	1.07209	0.783

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34606	0.23
27DAP/17DAP	0.89362	0.684
39DAP/27DAP	0.89411	0.556
41DAP/39DAP	0.81015	0.047
42DAP/41DAP	0.96518	0.732
43DAP/42DAP	0.74062	0.085
47DAP/43DAP	0.74362	0.259
52DAP/47DAP	1.46973	0.226
57DAP/52DAP	0.90997	0.514
57DAP/7DAP	0.86521	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94417	0.445
17DAP/reference	0.96747	0.389
27DAP/reference	1.04433	0.974
39DAP/reference	0.94307	0.307
41DAP/reference	0.96994	0.489
42DAP/reference	0.96852	0.371
43DAP/reference	0.97549	0.502
47DAP/reference	1.08523	0.458
52DAP/reference	0.94683	0.213
57DAP/reference	1.09567	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02402	0.951
17DAP/reference	1.25628	0.055
27DAP/reference	1.25012	0.203
39DAP/reference	1.51983	0.011
41DAP/reference	1.45864	0.011
42DAP/reference	1.24342	0.042
43DAP/reference	0.9538	0.468
47DAP/reference	1.01126	1
52DAP/reference	1.26304	0.043
57DAP/reference	1.08569	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90767	0.268
17DAP/reference	1.11884	0.261
27DAP/reference	1.14011	0.065
39DAP/reference	1.1268	0.254
41DAP/reference	1.13392	0.588
42DAP/reference	1.15331	0.701
43DAP/reference	1.38585	0.019
47DAP/reference	0.99749	0.646
52DAP/reference	1.0536	0.917
57DAP/reference	1.45043	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90386	1
26DAP/20DAP	0.78431	0.512
34DAP/26DAP	1.21943	0.819
51DAP/34DAP	0.52569
52DAP/51DAP	0.85623	1
53DAP/52DAP	0.72123	0.056
55DAP/53DAP	0.94015	0.686
57DAP/55DAP	1.18416	0.764
62DAP/57DAP	1.0184	1
68DAP/62DAP	0.84699	0.055
68DAP/14DAP	0.94285	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.54385	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.20641	0.058
Mature Green Tomato/Ripe Tomato	5.88856	0.015
Immature Eggplant/Mature Eggplant	1.75527
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17135	0.277
IL2-6/WTpooled	0.87282	0.473
IL7-5/WTpooled	1.41085	0.792
IL7-3/WTpooled	1.09394	1
IL12-4/WTpooled	1.01947	0.646
IL1-4/WTpooled	1.17968	1
WT/WTpooled	0.97119	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	0.98948	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92265	1
DC3000/delta hrp 6h	1.1353	1
DC3000/delta hrp 12h	1.33487	1
DC3000/delta hrp 24h	0.45698	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46833	0.023
DC3000 delta B/DC3000 delta AB	0.50651	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93676	1
Exp 36h	0.70259	0.539
Exp 60h	0.74024	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9963	1
Var 0h	1.21373	0.782
Var 12h I row2-row1	0.81424	0.338
Var 12h NI row2-row1	0.94543	0.713
Var 36h I row2-row1	1.00299	1
Var 36h NI row2-row1	1.26829	0.482
Var 60h I row2-row1	1.36367	0.543
Var 60h NI row2-row1	1.18457	0.904
Time course 0hI-0hNI	1.03953	0.852
Time course 12hI-12hNI	0.9484	0.682
Time course 36hI-36hNI	0.86438	0.102
Time course 60hI-60hNI	0.09197	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)	0.94363	0.662
transgenic ySAMdc/azygous control (breaker)	1.97776	0.166
transgenic ySAMdc/azygous control (red)	1.09138	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7627	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.53845	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.38665	0.083
Manapal/WT (break)	3.36627	0.14
Manapal/WT (red)	4.96471	0.126