Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.10.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91605	0.522
27DAP/17DAP	1.1114	0.872
39DAP/27DAP	0.98343	0.749
41DAP/39DAP	0.91379	0.636
42DAP/41DAP	1.03456	1
43DAP/42DAP	1.15162	0.954
47DAP/43DAP	1.10388	0.727
52DAP/47DAP	0.82775	0.551
57DAP/52DAP	0.9684	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93107	0.128
17DAP/reference	0.96877	0.147
27DAP/reference	0.95739	0.137
39DAP/reference	0.96551	0.391
41DAP/reference	0.91365	0.434
42DAP/reference	0.81389	0.002
43DAP/reference	0.97298	0.448
47DAP/reference	0.81048	0.001
52DAP/reference	0.81685	0.041
57DAP/reference	0.84461	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96267	0.716
27DAP/17DAP	0.98046	0.724
39DAP/27DAP	0.93601	0.382
41DAP/39DAP	0.97364	0.91
42DAP/41DAP	0.997	0.91
43DAP/42DAP	1.01265	0.746
47DAP/43DAP	0.96985	0.722
52DAP/47DAP	1.05328	0.816
57DAP/52DAP	0.9578	0.441
57DAP/7DAP	0.81811	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.12546	0.03
17DAP/reference	1.81092	0.016
27DAP/reference	2.69965	0.007
39DAP/reference	2.05207	0.014
41DAP/reference	2.69626	0.01
42DAP/reference	2.75676	0.016
43DAP/reference	3.21272	0.007
47DAP/reference	3.30565	0.404
52DAP/reference	19.5359	0.007
57DAP/reference	10.6932	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11287	0.384
17DAP/reference	0.9175	0.124
27DAP/reference	0.87395	0.104
39DAP/reference	0.90949	0.071
41DAP/reference	0.85839	0.057
42DAP/reference	0.71533	0.01
43DAP/reference	0.90944	0.336
47DAP/reference	0.77176	0.01
52DAP/reference	0.91675	0.047
57DAP/reference	0.99315	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	5.3204	0.017
17DAP/reference	0.98991	0.709
27DAP/reference	2.0599	0.042
39DAP/reference	7.12358	0.015
41DAP/reference	5.87041	0.013
42DAP/reference	3.093	0.03
43DAP/reference	2.25741	0.186
47DAP/reference	0.83592	0.093
52DAP/reference	2.47277	0.161
57DAP/reference	1.51753	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98865	1
26DAP/20DAP	1.03428	0.962
34DAP/26DAP	0.97257	0.92
51DAP/34DAP	1.27937	0.108
52DAP/51DAP	1.02309	0.77
53DAP/52DAP	1.04427	0.895
55DAP/53DAP	1.07826	0.855
57DAP/55DAP	0.88566	0.499
62DAP/57DAP	0.87584	0.871
68DAP/62DAP	0.94509	0.747
68DAP/14DAP	1.27293	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10059	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.382	0.018
Immature Eggplant/Mature Eggplant	0.32698	0.062
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	6.12632	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01379	1
1-1-2/M82	1.00059	1
12-2/M82	1.08823	1
12-4/M82	1.09632	1
1-3/M82	1.0244	1
2-1-1/M82	1.63755
2-1/M82	N/A	N/A
2-6/M82	1.07597	0.695
3-2/M82	0.90856	0.752
4-1-1/M82	1.1775	1
4-1/M82	1.27125	0.512
4-3-2/M82	1.0532	0.508
4-3/M82	1.04665	1
5-3/M82	0.99056	1
6-2/M82	0.94433	1
6-3/M82	0.96427	1
7-1/M82	1.02513
7-2/M82	1.13994	0.291
9-3-2/M82	0.99064	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91546	0.321
IL2-6/WTpooled	0.89134	1
IL7-5/WTpooled	1.37872	0.792
IL7-3/WTpooled	0.83776	0.294
IL12-4/WTpooled	0.96266	1
IL1-4/WTpooled	1.08677	1
WT/WTpooled	0.99484	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	0.85212	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98653	1
DC3000/delta hrp 6h	0.84509	0.95
DC3000/delta hrp 12h	1.09802	1
DC3000/delta hrp 24h	0.98808	0.966

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.93147	0.485
DC3000 delta B/DC3000 delta AB	0.99859	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98493	1
Exp 36h	1.16646	0.693
Exp 60h	0.89082	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.62291	0.332
Var 12h I row2-row1	1.01946	0.795
Var 12h NI row2-row1	1.02997	1
Var 36h I row2-row1	1.14041	0.601
Var 36h NI row2-row1	1.19158	1
Var 60h I row2-row1	1.25755
Var 60h NI row2-row1	0.97981	1
Time course 0hI-0hNI	1.05833	0.63
Time course 12hI-12hNI	1.00868	0.85
Time course 36hI-36hNI	0.97836	0.418
Time course 60hI-60hNI	0.76837	0.011

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)	1.40842	0.212
transgenic ySAMdc/azygous control (breaker)	0.70815	0.173
transgenic ySAMdc/azygous control (red)	0.92428	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01262	0.495

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15519	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14529	0.096
Manapal/WT (break)	1.03201	1
Manapal/WT (red)	1.1684	0.164