Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.3.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.91323	0.05
27DAP/17DAP	1.32543	0.761
39DAP/27DAP	1.59222	0.132
41DAP/39DAP	0.53986	0.041
42DAP/41DAP	2.50582	0.042
43DAP/42DAP	2.31543	0.121
47DAP/43DAP	2.13209	0.223
52DAP/47DAP	1.50987	0.516
57DAP/52DAP	1.75099	0.918

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59853	0.044
17DAP/reference	0.52463	0.009
27DAP/reference	0.79999	0.182
39DAP/reference	0.62206	0.017
41DAP/reference	0.47043	0.012
42DAP/reference	0.90196	0.188
43DAP/reference	2.70661
47DAP/reference	3.54196	0.175
52DAP/reference	6.56114	0.007
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27061	0.119
27DAP/17DAP	1.16867	0.645
39DAP/27DAP	1.14107	0.575
41DAP/39DAP	1.07085	0.91
42DAP/41DAP	1.7166	0.026
43DAP/42DAP	1.29708	0.122
47DAP/43DAP	1.19462	0.231
52DAP/47DAP	1.81108	0.081
57DAP/52DAP	1.40661	0.265
57DAP/7DAP	3.51978	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69181	0.091
17DAP/reference	0.74186	0.011
27DAP/reference	0.71511	0.012
39DAP/reference	0.82526	0.095
41DAP/reference	0.65213	0.019
42DAP/reference	0.78234	0.035
43DAP/reference	0.93322	0.351
47DAP/reference	0.90129	0.383
52DAP/reference	0.72263	0.049
57DAP/reference	0.60927	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43184	0.007
17DAP/reference	0.62301	0.006
27DAP/reference	1.24302	0.81
39DAP/reference	1.0265	0.702
41DAP/reference	0.72547	0.033
42DAP/reference	0.93726	0.355
43DAP/reference	0.49812	0.009
47DAP/reference	0.62905	0.008
52DAP/reference	0.53189	0.003
57DAP/reference	0.48684	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62334	0.033
17DAP/reference	0.84021	0.262
27DAP/reference	0.66211	0.024
39DAP/reference	0.895	0.101
41DAP/reference	0.88314	0.107
42DAP/reference	1.29581	0.443
43DAP/reference	2.12489	0.02
47DAP/reference	3.6392	0.005
52DAP/reference	4.0498	0.03
57DAP/reference	14.5521	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.64221	0.733
26DAP/20DAP	1.17077	0.471
34DAP/26DAP	1.02008	1
51DAP/34DAP	2.09351	0.046
52DAP/51DAP	1.0205	0.873
53DAP/52DAP	0.90547	0.498
55DAP/53DAP	0.86795	0.218
57DAP/55DAP	0.99325	0.93
62DAP/57DAP	2.00252	0.003
68DAP/62DAP	0.90373	0.722
68DAP/14DAP	1.77981	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	10.8574	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74791	0.213
Mature Green Tomato/Ripe Tomato	0.22912	0.016
Immature Eggplant/Mature Eggplant	0.85611	0.407
Ripe Pepper/Ripe Tomato	0.22828	0.224
Mature Eggplant/Ripe Tomato	0.07487	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.43775	0.574
1-1-2/M82	1.45291	1
12-2/M82	0.91438	0.74
12-4/M82	1.0452	1
1-3/M82	2.39512	0.277
2-1-1/M82	0.81071	0.565
2-1/M82	0.99402	1
2-6/M82	0.97588	1
3-2/M82	1.15383	0.717
4-1-1/M82	1.05336	1
4-1/M82	2.62312	0.853
4-3-2/M82	1.1873	0.262
4-3/M82	0.9776	1
5-3/M82	0.73035	0.447
6-2/M82	0.48257	0.481
6-3/M82	0.90923	1
7-1/M82	1.02314	1
7-2/M82	1.12075	1
9-3-2/M82	1.9492	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.96541	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.21018	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.64727
IL1-4/WTpooled	1.08708	1
WT/WTpooled	0.93516

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	0.80951	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06297	0.921
DC3000/delta hrp 6h	0.97075	0.95
DC3000/delta hrp 12h	1.31028	1
DC3000/delta hrp 24h	1.0156	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.68964	0.513
DC3000 delta B/DC3000 delta AB	0.65786	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92721	0.328
Exp 36h	1.33719	1
Exp 60h	1.29057	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99992	1
Var 0h	0.52752	1
Var 12h I row2-row1	0.80037	0.338
Var 12h NI row2-row1	0.95086	0.713
Var 36h I row2-row1	0.7833	0.805
Var 36h NI row2-row1	1.12286	1
Var 60h I row2-row1	1.14931	0.543
Var 60h NI row2-row1	1.1692	0.586
Time course 0hI-0hNI	0.93999	0.461
Time course 12hI-12hNI	0.97099	0.581
Time course 36hI-36hNI	0.83448	0.023
Time course 60hI-60hNI	0.23492	0.006

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)	1.20581	0.261
transgenic ySAMdc/azygous control (breaker)	1.2725	1
transgenic ySAMdc/azygous control (red)	1.03207	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97949	0.609

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.12361	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.82641	0.14
Manapal/WT (break)	1.08687	1
Manapal/WT (red)	0.20635	0.181