Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.16.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03809	0.919
27DAP/17DAP	1.10264	0.872
39DAP/27DAP	1.13078	0.894
41DAP/39DAP	0.85205	0.445
42DAP/41DAP	1.04064	0.992
43DAP/42DAP	1.12199	0.875
47DAP/43DAP	1.14401	0.769
52DAP/47DAP	0.92169	0.711
57DAP/52DAP	1.32002	0.894

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94809	0.308
17DAP/reference	0.99564	0.904
27DAP/reference	1.01205	0.88
39DAP/reference	0.99438	0.921
41DAP/reference	1.0615	0.287
42DAP/reference	0.93683	0.05
43DAP/reference	0.96436	0.448
47DAP/reference	0.95742	0.137
52DAP/reference	0.89055	0.131
57DAP/reference	1.0351	0.744

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91088	0.47
27DAP/17DAP	1.0114	1
39DAP/27DAP	0.91383	0.308
41DAP/39DAP	1.11937	0.69
42DAP/41DAP	1.03805	0.913
43DAP/42DAP	1.09957	0.554
47DAP/43DAP	1.22685	0.344
52DAP/47DAP	1.07704	0.831
57DAP/52DAP	1.26217	0.268
57DAP/7DAP	0.96743	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83553	0.1
17DAP/reference	0.81631	0.016
27DAP/reference	0.77526	0.01
39DAP/reference	0.86591	0.017
41DAP/reference	0.83394	0.047
42DAP/reference	0.8846	0.117
43DAP/reference	0.89461	0.069
47DAP/reference	0.94595	0.222
52DAP/reference	0.74708	0.011
57DAP/reference	0.73511	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97429	0.623
17DAP/reference	0.90587	0.011
27DAP/reference	0.92726	0.257
39DAP/reference	0.94767	0.25
41DAP/reference	0.89977	0.103
42DAP/reference	0.87356	0.098
43DAP/reference	1.01548	0.846
47DAP/reference	0.94476	0.021
52DAP/reference	0.95286	0.131
57DAP/reference	0.98971	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87817	0.055
17DAP/reference	0.95452	0.322
27DAP/reference	0.84005	0.047
39DAP/reference	0.88728	0.04
41DAP/reference	0.91343	0.237
42DAP/reference	0.90742	0.071
43DAP/reference	0.88099	0.095
47DAP/reference	0.98801	0.574
52DAP/reference	0.87618	0.303
57DAP/reference	0.84911	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96164	1
26DAP/20DAP	1.20646	0.487
34DAP/26DAP	0.83988	0.412
51DAP/34DAP	0.95067	0.799
52DAP/51DAP	0.85946	1
53DAP/52DAP	0.74616	0.402
55DAP/53DAP	1.18368	0.504
57DAP/55DAP	1.08895	0.881
62DAP/57DAP	0.96097	0.994
68DAP/62DAP	0.97993	0.863
68DAP/14DAP	0.93528	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06275	0.954

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13302	0.417
Mature Green Tomato/Ripe Tomato	0.61344	0.029
Immature Eggplant/Mature Eggplant	1.5704	0.053
Ripe Pepper/Ripe Tomato	1.59212	1
Mature Eggplant/Ripe Tomato	2.31816	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01854	1
1-1-2/M82	1.28195	1
12-2/M82	1.29141	0.61
12-4/M82	1.16061	1
1-3/M82	0.76152	0.378
2-1-1/M82	0.99936	1
2-1/M82	0.89012
2-6/M82	0.89929	1
3-2/M82	1.16228	0.549
4-1-1/M82	0.88716	1
4-1/M82	1.21606	1
4-3-2/M82	1.52153	0.508
4-3/M82	1.20671	1
5-3/M82	1.03097	1
6-2/M82	0.75622	1
6-3/M82	0.87506	1
7-1/M82	N/A	N/A
7-2/M82	0.95305	0.881
9-3-2/M82	1.56175	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.83588	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01394	0.921
DC3000/delta hrp 6h	1.03526	0.95
DC3000/delta hrp 12h	0.99946	1
DC3000/delta hrp 24h	1.08079	0.411

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	0.87975	0.418

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25266	1
Exp 36h	1.5245	0.409
Exp 60h	1.75208	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	1.09331	1
Var 0h	1.24876	0.936
Var 12h I row2-row1	1.2607	0.406
Var 12h NI row2-row1	0.98923	1
Var 36h I row2-row1	1.07802	1
Var 36h NI row2-row1	0.99104	0.852
Var 60h I row2-row1	0.99805	1
Var 60h NI row2-row1	1.0229	1
Time course 0hI-0hNI	1.00053	1
Time course 12hI-12hNI	1.02447	0.786
Time course 36hI-36hNI	0.95303	0.433
Time course 60hI-60hNI	1.24197	0.029

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)	1.01435	0.748
transgenic ySAMdc/azygous control (breaker)	1.20594	1
transgenic ySAMdc/azygous control (red)	1.18946	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00183	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94678	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85846	1
Manapal/WT (break)	0.8414	0.285
Manapal/WT (red)	0.79838	0.274