Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.8.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87293	0.445
27DAP/17DAP	0.94696	0.894
39DAP/27DAP	0.96722	0.719
41DAP/39DAP	1.18968	0.152
42DAP/41DAP	1.13362	0.856
43DAP/42DAP	1.01255	1
47DAP/43DAP	1.07616	0.569
52DAP/47DAP	1.02941	0.969
57DAP/52DAP	1.07328	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09382	0.5
17DAP/reference	0.91795	0.208
27DAP/reference	0.9255	0.339
39DAP/reference	0.92174	0.37
41DAP/reference	0.85191	0.026
42DAP/reference	1.00418	0.688
43DAP/reference	0.94482	0.377
47DAP/reference	0.95207	0.191
52DAP/reference	1.12436	0.256
57DAP/reference	1.02002	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99069	0.801
27DAP/17DAP	0.89322	0.39
39DAP/27DAP	1.01555	0.779
41DAP/39DAP	1.04186	0.773
42DAP/41DAP	0.98365	0.797
43DAP/42DAP	0.95742	0.558
47DAP/43DAP	0.99718	0.985
52DAP/47DAP	0.91175	0.397
57DAP/52DAP	1.05996	0.933
57DAP/7DAP	1.06891	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00478	1
17DAP/reference	1.19912	0.328
27DAP/reference	0.92932	0.375
39DAP/reference	0.95349	0.411
41DAP/reference	1.01548	1
42DAP/reference	0.96853	0.482
43DAP/reference	1.07854	0.483
47DAP/reference	1.04835	0.804
52DAP/reference	1.36496	0.033
57DAP/reference	1.23183	0.046

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0865	0.373
17DAP/reference	1.17765	0.338
27DAP/reference	0.9868	0.598
39DAP/reference	1.07836	0.602
41DAP/reference	0.95952	0.393
42DAP/reference	0.84483	0.067
43DAP/reference	0.94735	0.43
47DAP/reference	0.87944	0.038
52DAP/reference	1.03057	0.882
57DAP/reference	0.95978	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07718	0.456
17DAP/reference	1.02461	0.988
27DAP/reference	1.04116	0.871
39DAP/reference	1.09573	0.296
41DAP/reference	1.43629	0.411
42DAP/reference	1.15044	0.272
43DAP/reference	1.42806	0.069
47DAP/reference	1.01075	1
52DAP/reference	0.99732	0.763
57DAP/reference	1.22133	0.1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16397	0.966
26DAP/20DAP	1.05517	1
34DAP/26DAP	0.98031	0.988
51DAP/34DAP	1.0683	0.666
52DAP/51DAP	0.95969	1
53DAP/52DAP	0.85974	0.173
55DAP/53DAP	0.86571	0.111
57DAP/55DAP	1.19835	0.779
62DAP/57DAP	1.07452	0.868
68DAP/62DAP	1.26663	0.44
68DAP/14DAP	1.71258	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87862	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.68295	0.178
Mature Green Tomato/Ripe Tomato	1.04635	0.814
Immature Eggplant/Mature Eggplant	0.6991	0.064
Ripe Pepper/Ripe Tomato	2.39139	0.258
Mature Eggplant/Ripe Tomato	0.66686	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.81963	0.708
1-1-2/M82	0.97647	1
12-2/M82	0.83556	0.496
12-4/M82	0.84147	0.319
1-3/M82	1.11581	1
2-1-1/M82	1.01021	1
2-1/M82	1.13198
2-6/M82	1.2308	0.505
3-2/M82	1.11514	0.84
4-1-1/M82	1.05297	1
4-1/M82	0.99824
4-3-2/M82	0.99279	1
4-3/M82	0.91212	1
5-3/M82	1.11066	1
6-2/M82	N/A	N/A
6-3/M82	1.10742
7-1/M82	1.01917	1
7-2/M82	1.01801	1
9-3-2/M82	0.91368	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9041	1
IL2-6/WTpooled	1.58504	0.395
IL7-5/WTpooled	0.94853	1
IL7-3/WTpooled	0.77608	0.418
IL12-4/WTpooled	0.74062	0.478
IL1-4/WTpooled	1.00962	1
WT/WTpooled	0.92991	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	0.84514	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02175	0.921
DC3000/delta hrp 6h	0.97504	0.95
DC3000/delta hrp 12h	1.07427	1
DC3000/delta hrp 24h	0.78472	0.087

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01495	0.441
DC3000 delta B/DC3000 delta AB	1.02341	0.726

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16277	1
Exp 36h	1.36738	0.693
Exp 60h	1.115	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03324	1
Var 0h	0.86654	0.933
Var 12h I row2-row1	1.01142	1
Var 12h NI row2-row1	1.112	1
Var 36h I row2-row1	0.89476	1
Var 36h NI row2-row1	0.76312	0.549
Var 60h I row2-row1	4.16458	1
Var 60h NI row2-row1	0.91467	0.408
Time course 0hI-0hNI	0.92068	0.339
Time course 12hI-12hNI	0.9996	1
Time course 36hI-36hNI	1.11752	0.248
Time course 60hI-60hNI	0.76436	0.009

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)	1.02939	0.455
transgenic ySAMdc/azygous control (breaker)	1.84103	0.161
transgenic ySAMdc/azygous control (red)	1.2733	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02585	0.234

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81983	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13304	0.09
Manapal/WT (break)	1.47802	0.183
Manapal/WT (red)	1.52217	0.142