Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.7.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99232	0.911
27DAP/17DAP	1.17052	0.798
39DAP/27DAP	1.10957	0.915
41DAP/39DAP	0.92663	0.681
42DAP/41DAP	0.95679	1
43DAP/42DAP	1.05681	0.993
47DAP/43DAP	1.12659	0.405
52DAP/47DAP	0.93552	0.781
57DAP/52DAP	1.05228	0.95

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05098	0.265
17DAP/reference	0.97472	0.701
27DAP/reference	0.98284	0.525
39DAP/reference	1.09778	0.497
41DAP/reference	0.85253	0.114
42DAP/reference	1.03327	0.159
43DAP/reference	0.98497	0.82
47DAP/reference	1.03413	0.391
52DAP/reference	1.18632	0.302
57DAP/reference	1.27204	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09309	0.593
27DAP/17DAP	0.98261	0.887
39DAP/27DAP	0.97833	0.887
41DAP/39DAP	1.01645	0.914
42DAP/41DAP	1.06482	0.675
43DAP/42DAP	0.92816	0.132
47DAP/43DAP	1.06402	0.892
52DAP/47DAP	1.10283	0.713
57DAP/52DAP	0.86683	0.457
57DAP/7DAP	1.26013	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9233	0.224
17DAP/reference	0.78476	0.031
27DAP/reference	0.7718	0.01
39DAP/reference	0.8339	0.031
41DAP/reference	0.81968	0.019
42DAP/reference	0.77191	0.011
43DAP/reference	0.70342	0.011
47DAP/reference	0.88129	0.168
52DAP/reference	1.02282	0.781
57DAP/reference	0.86746	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9486	0.475
17DAP/reference	1.02898	0.644
27DAP/reference	0.97816	0.537
39DAP/reference	1.07647	0.848
41DAP/reference	1.19125	0.502
42DAP/reference	1.0049	1
43DAP/reference	0.93285	0.336
47DAP/reference	0.95665	0.126
52DAP/reference	1.0745	0.368
57DAP/reference	1.1655	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85718	0.049
17DAP/reference	0.92143	0.398
27DAP/reference	0.8395	0.062
39DAP/reference	0.80959	0.024
41DAP/reference	0.86279	0.019
42DAP/reference	0.75697	0.036
43DAP/reference	0.87423	0.095
47DAP/reference	0.9864	0.558
52DAP/reference	0.82028	0.2
57DAP/reference	1.22005	0.56

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99058	1
26DAP/20DAP	0.79366	0.512
34DAP/26DAP	0.91357	0.627
51DAP/34DAP	0.93778	0.681
52DAP/51DAP	1.01746	0.925
53DAP/52DAP	0.94836	0.817
55DAP/53DAP	1.09396	0.79
57DAP/55DAP	0.97411	0.888
62DAP/57DAP	0.9364	0.28
68DAP/62DAP	1.20376	0.866
68DAP/14DAP	1.05452	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.07287	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94757	0.658
Mature Green Tomato/Ripe Tomato	1.29263	0.237
Immature Eggplant/Mature Eggplant	1.68795	0.058
Ripe Pepper/Ripe Tomato	0.78326	0.293
Mature Eggplant/Ripe Tomato	0.72645	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.00268	1
1-1-2/M82	1.20182
12-2/M82	0.98214	1
12-4/M82	0.98627	1
1-3/M82	1.06074
2-1-1/M82	0.88956	0.465
2-1/M82	0.74224
2-6/M82	0.9687	1
3-2/M82	0.99425
4-1-1/M82	0.82438	1
4-1/M82	0.99542	1
4-3-2/M82	0.92297	0.487
4-3/M82	0.72623	0.578
5-3/M82	1.01001	1
6-2/M82	1.0705
6-3/M82	0.86015	1
7-1/M82	1.02927	1
7-2/M82	0.91677	0.796
9-3-2/M82	1.01337	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.15195
IL7-5/WTpooled	0.75583
IL7-3/WTpooled	1.01699	1
IL12-4/WTpooled	1.03126	1
IL1-4/WTpooled	0.86085	0.402
WT/WTpooled	0.8379	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	0.98744	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95288	1
DC3000/delta hrp 6h	1.10629	1
DC3000/delta hrp 12h	0.94875	1
DC3000/delta hrp 24h	1.2148	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91039	0.66
DC3000 delta B/DC3000 delta AB	0.89769	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06259	1
Exp 36h	1.29763	0.409
Exp 60h	1.0887	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97609	1
Var 0h	0.8221	1
Var 12h I row2-row1	0.89562	0.363
Var 12h NI row2-row1	1.07035	0.649
Var 36h I row2-row1	0.98821	1
Var 36h NI row2-row1	0.85437	0.645
Var 60h I row2-row1	0.90331	0.582
Var 60h NI row2-row1	0.90991	0.756
Time course 0hI-0hNI	1.02411	0.833
Time course 12hI-12hNI	0.99875	1
Time course 36hI-36hNI	1.04377	0.799
Time course 60hI-60hNI	0.88024	0.026

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)	0.65013	0.213
transgenic ySAMdc/azygous control (breaker)	1.36937	0.248
transgenic ySAMdc/azygous control (red)	0.83871	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97222	0.16

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27243	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12389	0.307
Manapal/WT (break)	0.5478	0.299
Manapal/WT (red)	0.70869	0.199