Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.6.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70336	0.103
27DAP/17DAP	0.88744	0.779
39DAP/27DAP	0.99514	0.798
41DAP/39DAP	1.06616	0.871
42DAP/41DAP	1.12684	0.913
43DAP/42DAP	1.16032	0.854
47DAP/43DAP	1.06916	0.769
52DAP/47DAP	0.94237	0.774
57DAP/52DAP	1.01904	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08244	0.994
17DAP/reference	0.7649
27DAP/reference	0.86335	0.304
39DAP/reference	0.694	0.031
41DAP/reference	0.49699	0.009
42DAP/reference	1.15501	0.241
43DAP/reference	0.83072	0.103
47DAP/reference	1.17317	0.391
52DAP/reference	1.94377	0.032
57DAP/reference	1.33398	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73392	0.035
27DAP/17DAP	0.89112	0.312
39DAP/27DAP	1.04642	0.663
41DAP/39DAP	1.20671	0.427
42DAP/41DAP	0.99455	0.84
43DAP/42DAP	1.06353	0.23
47DAP/43DAP	1.04885	0.837
52DAP/47DAP	0.92089	0.498
57DAP/52DAP	1.19734	0.533
57DAP/7DAP	0.975	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19356	0.057
17DAP/reference	1.36392	0.016
27DAP/reference	1.53126	0.008
39DAP/reference	0.98275	0.474
41DAP/reference	1.17307	0.023
42DAP/reference	1.11294	0.686
43DAP/reference	2.03437
47DAP/reference	1.10124	0.537
52DAP/reference	1.31422	0.021
57DAP/reference	1.66911	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01764	0.77
17DAP/reference	1.06044	0.999
27DAP/reference	1.20746	0.583
39DAP/reference	1.85287
41DAP/reference	1.15555	0.45
42DAP/reference	1.20887	0.17
43DAP/reference	0.88797	0.361
47DAP/reference	0.68661	0.019
52DAP/reference	1.55385	0.006
57DAP/reference	1.02593	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	1.6473	0.148
27DAP/reference	2.44834	0.054
39DAP/reference	2.59861	0.003
41DAP/reference	2.15017	0.009
42DAP/reference	1.36696	0.05
43DAP/reference	1.64248	0.014
47DAP/reference	1.08355	0.966
52DAP/reference	1.75396	0.061
57DAP/reference	1.45116	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05072	1
26DAP/20DAP	1.71012	0.101
34DAP/26DAP	0.87903	0.666
51DAP/34DAP	0.98358	0.698
52DAP/51DAP	1.01595	0.925
53DAP/52DAP	0.93775	0.741
55DAP/53DAP	1.02774	1
57DAP/55DAP	0.76542	0.222
62DAP/57DAP	2.11689
68DAP/62DAP	8.04573	0.151
68DAP/14DAP	10.1118	0.045

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18906	0.041

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.45727	0.063
Mature Green Tomato/Ripe Tomato	0.78898	0.377
Immature Eggplant/Mature Eggplant	1.00381	1
Ripe Pepper/Ripe Tomato	0.93056
Mature Eggplant/Ripe Tomato	9.2682	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07717	0.877
1-1-2/M82	0.99624	1
12-2/M82	0.98123	1
12-4/M82	0.97009	1
1-3/M82	0.95698	0.33
2-1-1/M82	1.12163	0.439
2-1/M82	1.23009	1
2-6/M82	1.11465	0.452
3-2/M82	0.95659
4-1-1/M82	1.02801	1
4-1/M82	0.67035	0.665
4-3-2/M82	1.28107	0.241
4-3/M82	0.8732	0.578
5-3/M82	0.90027	1
6-2/M82	1.0869	1
6-3/M82	0.92938	1
7-1/M82	0.8625	0.803
7-2/M82	1.02679	1
9-3-2/M82	0.96909	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.21761	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94536	1
DC3000/delta hrp 6h	0.97098	0.95
DC3000/delta hrp 12h	1.02093	1
DC3000/delta hrp 24h	1.13744	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.01086	0.03
DC3000 delta B/DC3000 delta AB	1.01273	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94978	1
Exp 36h	1.23557	1
Exp 60h	1.02988	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96352	1
Var 0h	1.08429	0.936
Var 12h I row2-row1	0.97788	0.948
Var 12h NI row2-row1	1.0068	1
Var 36h I row2-row1	1.12883	0.908
Var 36h NI row2-row1	0.89617	0.743
Var 60h I row2-row1	0.944	0.952
Var 60h NI row2-row1	0.83109	0.38
Time course 0hI-0hNI	0.82306	0.053
Time course 12hI-12hNI	1.04343	0.63
Time course 36hI-36hNI	1.07249	0.975
Time course 60hI-60hNI	1.10169	0.254

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)	0.99982	1
transgenic ySAMdc/azygous control (breaker)	1.35047	1
transgenic ySAMdc/azygous control (red)	1.43334	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03469	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0881	0.307
Manapal/WT (break)	1.08571	1
Manapal/WT (red)	1.30254	0.164