Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.4.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17489	0.545
27DAP/17DAP	0.4978	0.032
39DAP/27DAP	0.79925	0.474
41DAP/39DAP	0.69687	0.126
42DAP/41DAP	0.75079	1
43DAP/42DAP	1.36518	0.475
47DAP/43DAP	0.43539	0.065
52DAP/47DAP	1.28487	0.811
57DAP/52DAP	1.19801	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72714	0.077
17DAP/reference	0.46733	0.007
27DAP/reference	0.49748	0.013
39DAP/reference	0.25895	0.007
41DAP/reference	0.21607	0.008
42DAP/reference	0.394	0.001
43DAP/reference	0.22793
47DAP/reference	0.34221	0.015
52DAP/reference	0.21835	0.01
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82672	0.036
27DAP/17DAP	0.76407	0.187
39DAP/27DAP	0.38222	0.029
41DAP/39DAP	1.27245	0.119
42DAP/41DAP	0.72697	0.02
43DAP/42DAP	0.64545	0.022
47DAP/43DAP	0.91391	0.382
52DAP/47DAP	1.18515	0.639
57DAP/52DAP	0.96211	0.673
57DAP/7DAP	0.53328	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10352	0.452
17DAP/reference	0.89073	0.035
27DAP/reference	0.78819	0.014
39DAP/reference	0.6354	0.011
41DAP/reference	0.50853	0.015
42DAP/reference	0.60916	0.01
43DAP/reference	0.52619	0.01
47DAP/reference	0.36493	0.032
52DAP/reference	0.59683	0.012
57DAP/reference	0.56474	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.47261	0.016
17DAP/reference	0.40099	0.007
27DAP/reference	0.56378	0.023
39DAP/reference	0.29942	0.008
41DAP/reference	1.06701	0.373
42DAP/reference	0.44841	0.01
43DAP/reference	0.44279	0.008
47DAP/reference	0.32819	0.007
52DAP/reference	0.26835	0.003
57DAP/reference	0.22132	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.04357	0.016
17DAP/reference	1.71822	0.133
27DAP/reference	1.28954	0.04
39DAP/reference	1.13445	0.353
41DAP/reference	0.83601	0.032
42DAP/reference	0.6058	0.036
43DAP/reference	0.62591	0.016
47DAP/reference	0.30138	0.004
52DAP/reference	0.51162	0.097
57DAP/reference	0.76526	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16448	0.966
26DAP/20DAP	0.9768	1
34DAP/26DAP	0.84866	0.412
51DAP/34DAP	0.40656	0.049
52DAP/51DAP	0.86839	1
53DAP/52DAP	0.7234	0.088
55DAP/53DAP	0.68943	0.064
57DAP/55DAP	1.27319	0.906
62DAP/57DAP	0.78485
68DAP/62DAP	1.3811	0.912
68DAP/14DAP	0.5124	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.33793	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.64461	0.058
Mature Green Tomato/Ripe Tomato	18.1546	0.015
Immature Eggplant/Mature Eggplant	0.38343	0.062
Ripe Pepper/Ripe Tomato	8.13794	0.256
Mature Eggplant/Ripe Tomato	20.5991	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02976	1
12-2/M82	0.9889	1
12-4/M82	0.71593	0.257
1-3/M82	1.82202
2-1-1/M82	0.79648
2-1/M82	N/A	N/A
2-6/M82	2.43601	0.452
3-2/M82	1.38078
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.62176
5-3/M82	0.97402	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.10977	1
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15438	0.277
IL2-6/WTpooled	1.229
IL7-5/WTpooled	1.2674	0.75
IL7-3/WTpooled	1.04291	0.362
IL12-4/WTpooled	0.8109	0.581
IL1-4/WTpooled	1.12211	1
WT/WTpooled	0.83567	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	1.01554	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9419	0.839
DC3000/delta hrp 6h	0.92221	0.95
DC3000/delta hrp 12h	0.77125	1
DC3000/delta hrp 24h	0.80018

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71719	0.042
DC3000 delta B/DC3000 delta AB	0.50209	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08637	1
Exp 36h	0.88713	0.749
Exp 60h	0.90147	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01704	1
Var 0h	1.20062	0.374
Var 12h I row2-row1	0.76922	0.338
Var 12h NI row2-row1	0.87946	0.546
Var 36h I row2-row1	0.76516	0.805
Var 36h NI row2-row1	1.27901	0.482
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	1.15334	0.904
Time course 0hI-0hNI	1.01737	0.867
Time course 12hI-12hNI	0.89033	0.116
Time course 36hI-36hNI	0.74128	0.023
Time course 60hI-60hNI	0.1012	0.005

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)	1.11957	0.863
transgenic ySAMdc/azygous control (breaker)	2.45407	0.161
transgenic ySAMdc/azygous control (red)	1.29287	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.51711	0.081

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.94357	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	15.8702	0.083
Manapal/WT (break)	3.61952	0.123
Manapal/WT (red)	1.3708	0.413