Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98884	0.83
27DAP/17DAP	1.07935	0.88
39DAP/27DAP	0.83496	0.522
41DAP/39DAP	1.45327	0.352
42DAP/41DAP	0.9741	1
43DAP/42DAP	1.10165	1
47DAP/43DAP	1.07052	0.873
52DAP/47DAP	0.85562	0.615
57DAP/52DAP	1.01624	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62777	0.027
17DAP/reference	0.69985	0.009
27DAP/reference	0.75334	0.047
39DAP/reference	0.83657	0.146
41DAP/reference	0.63887	0.039
42DAP/reference	0.73804	0.004
43DAP/reference	0.9141	0.088
47DAP/reference	0.7392	0.001
52DAP/reference	0.70827	0.016
57DAP/reference	0.84082	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84292	0.311
27DAP/17DAP	1.07447	0.798
39DAP/27DAP	1.14329	0.27
41DAP/39DAP	1.12286	0.735
42DAP/41DAP	0.83132	0.135
43DAP/42DAP	1.123	0.035
47DAP/43DAP	0.93395	0.597
52DAP/47DAP	1.04991	0.831
57DAP/52DAP	0.99557	0.833
57DAP/7DAP	0.99501	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84366	0.07
17DAP/reference	0.84572	0.024
27DAP/reference	0.93092	0.066
39DAP/reference	0.8518	0.014
41DAP/reference	0.9641	0.375
42DAP/reference	0.90161	0.023
43DAP/reference	0.8626	0.021
47DAP/reference	0.88083	0.168
52DAP/reference	1.00748	1
57DAP/reference	0.81369	0.052

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60342	0.007
17DAP/reference	0.55897	0.003
27DAP/reference	0.5834	0.007
39DAP/reference	0.64204	0.009
41DAP/reference	0.74816	0.026
42DAP/reference	0.75799	0.05
43DAP/reference	0.83261	0.039
47DAP/reference	0.90323	0.068
52DAP/reference	0.63779	0.004
57DAP/reference	0.59359	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85857	0.041
17DAP/reference	0.80864	0.13
27DAP/reference	0.80914	0.039
39DAP/reference	0.75531	0.008
41DAP/reference	1.02226	0.984
42DAP/reference	0.94971	0.22
43DAP/reference	0.85494	0.116
47DAP/reference	0.7727	0.008
52DAP/reference	0.64851	0.061
57DAP/reference	0.79392	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03557	0.966
26DAP/20DAP	1.05768	0.785
34DAP/26DAP	1.17161	0.542
51DAP/34DAP	1.17503	0.215
52DAP/51DAP	1.18341	0.51
53DAP/52DAP	1.10438	0.47
55DAP/53DAP	1.22669	0.46
57DAP/55DAP	1.06373	0.955
62DAP/57DAP	1.04515	1
68DAP/62DAP	1.08606	0.778
68DAP/14DAP	1.33086	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65503	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.997	0.835
Immature Eggplant/Mature Eggplant	1.35373	0.363
Ripe Pepper/Ripe Tomato	0.46906	0.224
Mature Eggplant/Ripe Tomato	0.70238	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92062	0.634
1-1-2/M82	0.96177	1
12-2/M82	1.31779
12-4/M82	0.92197	1
1-3/M82	1.21612	0.479
2-1-1/M82	0.66799
2-1/M82	N/A	N/A
2-6/M82	0.95927	1
3-2/M82	N/A	N/A
4-1-1/M82	1.03011	1
4-1/M82	1.41916
4-3-2/M82	0.92225	0.698
4-3/M82	0.88759
5-3/M82	1.26237	0.572
6-2/M82	1.67806
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.10271	0.385
9-3-2/M82	0.63892	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.13396	0.277
IL2-6/WTpooled	0.89427	0.473
IL7-5/WTpooled	1.02182	1
IL7-3/WTpooled	1.11009	1
IL12-4/WTpooled	1.1096	0.531
IL1-4/WTpooled	1.07761	1
WT/WTpooled	1.032	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	0.99339	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91855	1
DC3000/delta hrp 6h	0.7614
DC3000/delta hrp 12h	0.98802	1
DC3000/delta hrp 24h	0.93998	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76413	0.053
DC3000 delta B/DC3000 delta AB	1.04349	0.771

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.27619	1
Exp 36h	1.23106	1
Exp 60h	1.07629	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99101	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.90012	0.514
Var 12h NI row2-row1	1.42506	0.34
Var 36h I row2-row1	1.51926	0.339
Var 36h NI row2-row1	0.60026	0.478
Var 60h I row2-row1	1.55041	0.562
Var 60h NI row2-row1	0.73529	0.483
Time course 0hI-0hNI	1.13338	0.799
Time course 12hI-12hNI	1.03565	1
Time course 36hI-36hNI	2.15218	0.005
Time course 60hI-60hNI	1.89653	0.115

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)	1.28895	0.286
transgenic ySAMdc/azygous control (breaker)	2.49667	0.248
transgenic ySAMdc/azygous control (red)	0.78331	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9253	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.43172	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.61461	1
Manapal/WT (break)	0.85195	1
Manapal/WT (red)	0.77582	0.315