Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.7.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15702	0.656
27DAP/17DAP	0.60077	0.041
39DAP/27DAP	0.97923	0.749
41DAP/39DAP	0.58875	0.045
42DAP/41DAP	1.0366	1
43DAP/42DAP	1.01113	1
47DAP/43DAP	0.8412	0.473
52DAP/47DAP	0.84673	0.554
57DAP/52DAP	1.02645	0.972

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22652	0.241
17DAP/reference	1.01839	0.858
27DAP/reference	0.95397	0.538
39DAP/reference	0.77939	0.146
41DAP/reference	0.49909	0.009
42DAP/reference	0.79457	0.004
43DAP/reference	0.65111	0.022
47DAP/reference	0.61412	0.001
52DAP/reference	0.54106	0.025
57DAP/reference	0.75725	0.015

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42271	0.121
27DAP/17DAP	0.91071	0.782
39DAP/27DAP	0.43571	0.029
41DAP/39DAP	1.27995	0.469
42DAP/41DAP	0.92047	0.453
43DAP/42DAP	0.5689	0.022
47DAP/43DAP	0.85938	0.048
52DAP/47DAP	0.90262	0.553
57DAP/52DAP	1.06285	0.941
57DAP/7DAP	0.35434	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.656	0.024
17DAP/reference	0.94687	0.22
27DAP/reference	0.81528	0.031
39DAP/reference	0.69958	0.015
41DAP/reference	0.70232	0.022
42DAP/reference	0.60598	0.01
43DAP/reference	0.55384	0.011
47DAP/reference	0.60209	0.05
52DAP/reference	0.74408	0.027
57DAP/reference	0.70644	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94665	0.548
17DAP/reference	0.9836	0.548
27DAP/reference	1.40643	0.078
39DAP/reference	0.83602	0.159
41DAP/reference	1.11774	0.471
42DAP/reference	0.89228	0.098
43DAP/reference	0.58803	0.018
47DAP/reference	0.7151	0.032
52DAP/reference	0.61054	0.006
57DAP/reference	0.40056	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.47649	0.015
17DAP/reference	2.48757	0.07
27DAP/reference	1.99195	0.014
39DAP/reference	1.42088	0.019
41DAP/reference	1.108	0.537
42DAP/reference	0.93853	0.552
43DAP/reference	1.11655	0.721
47DAP/reference	0.77048	0.089
52DAP/reference	0.55001	0.053
57DAP/reference	2.95766	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0019	1
26DAP/20DAP	1.02397	1
34DAP/26DAP	0.83576	0.44
51DAP/34DAP	1.08749	0.925
52DAP/51DAP	1.63079	0.335
53DAP/52DAP	1.21878	0.343
55DAP/53DAP	0.97414	0.796
57DAP/55DAP	0.95316	0.765
62DAP/57DAP	0.89768	0.466
68DAP/62DAP	1.75964	0.052
68DAP/14DAP	1.31787	0.108

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.47907	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.46577	0.058
Mature Green Tomato/Ripe Tomato	2.42273	0.016
Immature Eggplant/Mature Eggplant	0.49405	0.057
Ripe Pepper/Ripe Tomato	3.45568	0.258
Mature Eggplant/Ripe Tomato	21.2702	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93059	0.944
1-1-2/M82	1.21372	1
12-2/M82	0.36236
12-4/M82	1.27439	1
1-3/M82	1.14159
2-1-1/M82	0.57514
2-1/M82	N/A	N/A
2-6/M82	1.38416
3-2/M82	1.0571	0.84
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.19861	1
4-3/M82	1.38549	0.268
5-3/M82	1.55062	0.572
6-2/M82	1.22136
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.12176	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.18533	0.277
IL2-6/WTpooled	1.16717	0.419
IL7-5/WTpooled	0.75588	1
IL7-3/WTpooled	1.06573	1
IL12-4/WTpooled	1.15162	0.673
IL1-4/WTpooled	0.94333	0.834
WT/WTpooled	1.01927	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	1.07045	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95771	1
DC3000/delta hrp 6h	0.96428	0.95
DC3000/delta hrp 12h	0.9668	1
DC3000/delta hrp 24h	0.90866	0.575

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62694	0.05
DC3000 delta B/DC3000 delta AB	0.45526	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01892	1
Exp 36h	1.00077	1
Exp 60h	0.96892	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96049	1
Var 0h	0.61473	1
Var 12h I row2-row1	0.8615	0.363
Var 12h NI row2-row1	0.97856	0.906
Var 36h I row2-row1	1.00137	1
Var 36h NI row2-row1	1.03775	1
Var 60h I row2-row1	1.12187	1
Var 60h NI row2-row1	1.00876	1
Time course 0hI-0hNI	0.95842	0.745
Time course 12hI-12hNI	0.98657	0.931
Time course 36hI-36hNI	0.9386	0.284
Time course 60hI-60hNI	0.3394	0.007

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)	1.13465	0.699
transgenic ySAMdc/azygous control (breaker)	5.22265	0.162
transgenic ySAMdc/azygous control (red)	1.57242	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.62978	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.83193	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.77923	0.096
Manapal/WT (break)	6.3576	0.14
Manapal/WT (red)	7.01842	0.133