Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.2.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06217	0.912
27DAP/17DAP	1.1441	0.849
39DAP/27DAP	1.00009	0.899
41DAP/39DAP	0.88	0.611
42DAP/41DAP	0.96903	0.397
43DAP/42DAP	0.93026	0.786
47DAP/43DAP	1.19755	0.282
52DAP/47DAP	0.72918	0.489
57DAP/52DAP	1.04437	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02242	0.71
17DAP/reference	1.05996	0.051
27DAP/reference	1.04477	0.179
39DAP/reference	1.03875	0.534
41DAP/reference	1.03336	0.241
42DAP/reference	0.96227	0.134
43DAP/reference	1.01568	0.866
47DAP/reference	1.05325	0.081
52DAP/reference	1.04463	0.633
57DAP/reference	1.09065	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15321	0.218
27DAP/17DAP	1.10019	0.541
39DAP/27DAP	0.84073	0.123
41DAP/39DAP	1.32927	0.868
42DAP/41DAP	1.20348	0.635
43DAP/42DAP	1.07877	0.478
47DAP/43DAP	0.93984	0.764
52DAP/47DAP	0.97738	0.902
57DAP/52DAP	0.816	0.103
57DAP/7DAP	1.05213	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1234	0.351
17DAP/reference	1.13097	0.162
27DAP/reference	1.32835	0.014
39DAP/reference	1.27939	0.022
41DAP/reference	1.07808	0.43
42DAP/reference	1.28203	0.076
43DAP/reference	3.08837	0.344
47DAP/reference	1.04515	0.822
52DAP/reference	1.18921	0.02
57DAP/reference	1.24403	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96158	0.457
17DAP/reference	1.02473	0.484
27DAP/reference	0.9751	0.554
39DAP/reference	1.03615	0.543
41DAP/reference	1.06847	0.353
42DAP/reference	1.02831	0.794
43DAP/reference	0.93921	0.37
47DAP/reference	0.9849	0.368
52DAP/reference	0.96699	0.239
57DAP/reference	0.99808	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.997	0.75
17DAP/reference	1.09954	0.65
27DAP/reference	1.40018	0.027
39DAP/reference	1.16947	0.018
41DAP/reference	1.21023	0.039
42DAP/reference	0.98998	0.816
43DAP/reference	1.22046	0.198
47DAP/reference	1.13741	0.028
52DAP/reference	1.08233	0.549
57DAP/reference	1.12107	0.228

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.83385
26DAP/20DAP	0.97215	1
34DAP/26DAP	1.00559	1
51DAP/34DAP	0.99607	0.937
52DAP/51DAP	0.85481	0.151
53DAP/52DAP	1.06601	0.502
55DAP/53DAP	0.99544	0.908
57DAP/55DAP	1.35345	0.094
62DAP/57DAP	0.96024	0.466
68DAP/62DAP	0.89234	0.722
68DAP/14DAP	1.09323	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.30722	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13384	0.287
Mature Green Tomato/Ripe Tomato	1.01154	0.835
Immature Eggplant/Mature Eggplant	1.05383	0.58
Ripe Pepper/Ripe Tomato	0.51718	0.224
Mature Eggplant/Ripe Tomato	0.69212	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.2689	0.505
1-1-2/M82	1.08655
12-2/M82	0.99775	1
12-4/M82	1.01911	1
1-3/M82	1.42415	0.277
2-1-1/M82	1.11186	0.689
2-1/M82	0.6552	0.322
2-6/M82	1.10978	0.395
3-2/M82	1.07093	0.84
4-1-1/M82	1.12393	1
4-1/M82	1.22507	0.853
4-3-2/M82	1.10088	1
4-3/M82	1.32919	0.268
5-3/M82	0.99993	1
6-2/M82	1.1446
6-3/M82	1.0626	1
7-1/M82	1.07089	1
7-2/M82	1.11369	1
9-3-2/M82	0.98912	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73294
IL2-6/WTpooled	1.78877	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98887	1
IL12-4/WTpooled	1.02587	1
IL1-4/WTpooled	0.89048
WT/WTpooled	1.0585	0.89

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	0.95584	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0716	0.894
DC3000/delta hrp 6h	1.10004	0.95
DC3000/delta hrp 12h	0.91733	1
DC3000/delta hrp 24h	1.01778	1

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	1.08505	0.539

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95557	1
Exp 36h	1.01535	1
Exp 60h	1.08202	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98231	1
Var 0h	1.1308	0.782
Var 12h I row2-row1	1.0333	0.795
Var 12h NI row2-row1	1.23968	0.649
Var 36h I row2-row1	1.36585	0.742
Var 36h NI row2-row1	0.67022	0.706
Var 60h I row2-row1	0.91677	0.832
Var 60h NI row2-row1	0.99907	1
Time course 0hI-0hNI	0.99483	1
Time course 12hI-12hNI	1.04715	0.654
Time course 36hI-36hNI	1.12167	0.128
Time course 60hI-60hNI	1.32528	0.013

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)	0.76753	0.299
transgenic ySAMdc/azygous control (breaker)	0.90448	0.49
transgenic ySAMdc/azygous control (red)	1.04346	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00994	0.619

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14571	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8892	1
Manapal/WT (break)	0.79213	0.299
Manapal/WT (red)	1.46126	0.222