Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.20.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45058	0.394
27DAP/17DAP	1.14105	0.849
39DAP/27DAP	0.87734	0.537
41DAP/39DAP	0.80166	0.308
42DAP/41DAP	0.77616	0.774
43DAP/42DAP	1.14759	1
47DAP/43DAP	1.36044	0.538
52DAP/47DAP	0.96521	0.87
57DAP/52DAP	1.37286	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93607	0.262
17DAP/reference	1.04299	0.248
27DAP/reference	1.08218	0.109
39DAP/reference	1.06809	0.129
41DAP/reference	0.96497	0.667
42DAP/reference	0.97123	0.268
43DAP/reference	0.93046	0.36
47DAP/reference	1.00733	1
52DAP/reference	0.87373	0.152
57DAP/reference	0.93385	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95228	0.454
27DAP/17DAP	0.99274	0.943
39DAP/27DAP	0.99048	0.977
41DAP/39DAP	1.03602	0.763
42DAP/41DAP	1.04335	0.539
43DAP/42DAP	1.03915	0.478
47DAP/43DAP	0.98244	0.909
52DAP/47DAP	0.99302	0.947
57DAP/52DAP	1.01092	1
57DAP/7DAP	1.0252	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50698	0.126
17DAP/reference	2.45598	0.006
27DAP/reference	2.03117	0.008
39DAP/reference	2.46843	0.005
41DAP/reference	2.40937	0.011
42DAP/reference	2.82001	0.006
43DAP/reference	3.66056	0.007
47DAP/reference	2.20501	0.13
52DAP/reference	2.66506	0.007
57DAP/reference	2.78653	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96179	0.518
17DAP/reference	0.98313	0.499
27DAP/reference	0.83639	0.05
39DAP/reference	0.8782	0.152
41DAP/reference	1.1109	0.573
42DAP/reference	1.04059	0.476
43DAP/reference	0.85244	0.175
47DAP/reference	1.02295	0.712
52DAP/reference	0.9756	0.259
57DAP/reference	0.91224	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.75497	0.023
17DAP/reference	1.34585	0.545
27DAP/reference	2.56628	0.027
39DAP/reference	2.7482	0.008
41DAP/reference	2.06387	0.013
42DAP/reference	2.17395	0.057
43DAP/reference	2.26136	0.053
47DAP/reference	1.01714	1
52DAP/reference	2.64031	0.052
57DAP/reference	1.55779	0.842

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0585	0.43
26DAP/20DAP	0.86875	0.228
34DAP/26DAP	0.99419	1
51DAP/34DAP	0.96896	0.727
52DAP/51DAP	0.95567	1
53DAP/52DAP	1.02256	1
55DAP/53DAP	0.94394	0.604
57DAP/55DAP	1.12044	0.51
62DAP/57DAP	0.97884	0.994
68DAP/62DAP	0.82916	0.579
68DAP/14DAP	0.84182	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9212	0.166

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.67207	0.075
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.1635	0.222
Ripe Pepper/Ripe Tomato	1.94599	1
Mature Eggplant/Ripe Tomato	1.88514	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04236	1
1-1-2/M82	0.93245	0.958
12-2/M82	0.97692	0.955
12-4/M82	0.99762	0.619
1-3/M82	0.96534	0.501
2-1-1/M82	1.17003	0.764
2-1/M82	1.33557	1
2-6/M82	0.94096	1
3-2/M82	1.06004
4-1-1/M82	1.03376	1
4-1/M82	0.92448
4-3-2/M82	1.16698
4-3/M82	1.02598	1
5-3/M82	1.06171	1
6-2/M82	0.95464	0.497
6-3/M82	0.99802	1
7-1/M82	1.00198
7-2/M82	0.98462	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97903
IL2-6/WTpooled	0.93655	1
IL7-5/WTpooled	1.36245	0.75
IL7-3/WTpooled	1.03476	1
IL12-4/WTpooled	1.1856	0.538
IL1-4/WTpooled	1.05153	1
WT/WTpooled	1.1668	0.999

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	1.02099	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97404	1
DC3000/delta hrp 6h	1.03729	0.95
DC3000/delta hrp 12h	1.05801	1
DC3000/delta hrp 24h	0.99329	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1333	0.087
DC3000 delta B/DC3000 delta AB	1.15676	0.226

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24947	1
Exp 36h	1.14276	1
Exp 60h	0.994	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98505	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.77458	0.406
Var 12h NI row2-row1	1.02371	1
Var 36h I row2-row1	1.03421	1
Var 36h NI row2-row1	0.95571	0.584
Var 60h I row2-row1	1.0006	1
Var 60h NI row2-row1	1.08295	0.904
Time course 0hI-0hNI	0.98494	0.97
Time course 12hI-12hNI	1.06741	0.445
Time course 36hI-36hNI	0.99616	0.753
Time course 60hI-60hNI	1.29154	0.008

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)	1.2495	0.3
transgenic ySAMdc/azygous control (breaker)	1.27723	1
transgenic ySAMdc/azygous control (red)	1.36076	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00464	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.68811	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95895	1
Manapal/WT (break)	0.72962	0.333
Manapal/WT (red)	0.76838	0.216