Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.5.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10097	0.911
27DAP/17DAP	1.14746	0.825
39DAP/27DAP	0.89899	0.549
41DAP/39DAP	0.96122	0.791
42DAP/41DAP	1.06385	0.931
43DAP/42DAP	1.07323	0.968
47DAP/43DAP	1.20462	0.444
52DAP/47DAP	0.95096	0.812
57DAP/52DAP	0.99443	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38763	0.018
17DAP/reference	1.33446	0.045
27DAP/reference	1.1181	0.587
39DAP/reference	1.22979	0.197
41DAP/reference	1.53574	0.021
42DAP/reference	1.35481	0.001
43DAP/reference	1.10392	0.547
47DAP/reference	1.43557	0.004
52DAP/reference	0.72685	0.049
57DAP/reference	0.85058	0.068

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22239	0.5
27DAP/17DAP	0.93222	0.782
39DAP/27DAP	1.0581	0.793
41DAP/39DAP	0.97492	0.968
42DAP/41DAP	1.13769	0.46
43DAP/42DAP	0.83689	0.082
47DAP/43DAP	0.89546	0.439
52DAP/47DAP	0.81893	0.433
57DAP/52DAP	0.99724	0.848
57DAP/7DAP	0.84402	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99747	0.758
17DAP/reference	1.03726	0.754
27DAP/reference	1.0979	0.453
39DAP/reference	1.114	0.267
41DAP/reference	0.95396	0.284
42DAP/reference	1.21291	0.308
43DAP/reference	1.288	0.07
47DAP/reference	1.40722	0.059
52DAP/reference	0.99852	0.571
57DAP/reference	1.09705	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69011	0.055
17DAP/reference	1.62632	0.011
27DAP/reference	1.1522	0.116
39DAP/reference	1.20271	1
41DAP/reference	1.28032	0.055
42DAP/reference	1.00085	0.655
43DAP/reference	1.39054	0.14
47DAP/reference	1.32592	0.008
52DAP/reference	1.12138	0.667
57DAP/reference	1.28835	0.036

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94322	0.23
17DAP/reference	1.09358	0.865
27DAP/reference	1.31478	0.036
39DAP/reference	1.26551	0.022
41DAP/reference	1.0843	0.383
42DAP/reference	1.21518	0.265
43DAP/reference	0.86047	0.197
47DAP/reference	1.27812	0.099
52DAP/reference	1.44428	0.301
57DAP/reference	0.76001	0.154

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.71618
26DAP/20DAP	1.20222	0.718
34DAP/26DAP	1.00742	1
51DAP/34DAP	1.3039	0.051
52DAP/51DAP	0.6901	0.151
53DAP/52DAP	0.98369	0.917
55DAP/53DAP	0.7362	0.077
57DAP/55DAP	1.48063	0.079
62DAP/57DAP	1.36303	0.002
68DAP/62DAP	1.67912	0.464
68DAP/14DAP	0.83614

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94325	0.443

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.50381	0.07
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.19007
Mature Eggplant/Ripe Tomato	0.71214	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30685	0.591
1-1-2/M82	1.30827	0.977
12-2/M82	1.16165	1
12-4/M82	0.84137	1
1-3/M82	2.98405	1
2-1-1/M82	1.30807
2-1/M82	1.04616	1
2-6/M82	2.0844	0.385
3-2/M82	1.19602	0.84
4-1-1/M82	3.32251	0.968
4-1/M82	1.197	1
4-3-2/M82	1.7442	1
4-3/M82	1.95301	1
5-3/M82	0.96371	1
6-2/M82	3.8944	0.253
6-3/M82	1.1031	1
7-1/M82	0.93662	1
7-2/M82	1.18927	1
9-3-2/M82	1.10111	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.43069	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.76808
IL7-3/WTpooled	1.31806	0.362
IL12-4/WTpooled	0.87872	1
IL1-4/WTpooled	1.0058
WT/WTpooled	0.9101	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	1.06422	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99446	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.86789
DC3000/delta hrp 24h	2.96508	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.83713
DC3000 delta B/DC3000 delta AB	1.10893

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96683	1
Var 0h	0.91453	1
Var 12h I row2-row1	1.11668	0.736
Var 12h NI row2-row1	1.01968	1
Var 36h I row2-row1	1.13254	0.368
Var 36h NI row2-row1	0.95376	0.61
Var 60h I row2-row1	0.73871	0.287
Var 60h NI row2-row1	0.9542	1
Time course 0hI-0hNI	0.95789	0.675
Time course 12hI-12hNI	1.01579	0.876
Time course 36hI-36hNI	1.11479	0.044
Time course 60hI-60hNI	1.86395	0.008

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)	0.88024	0.529
transgenic ySAMdc/azygous control (breaker)	0.78238	0.49
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10058	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.46438	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.21647	0.13
Manapal/WT (red)	1.43229	0.222