Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09306	0.755
27DAP/17DAP	1.0613	0.895
39DAP/27DAP	1.33094	0.779
41DAP/39DAP	0.96522	0.83
42DAP/41DAP	1.25913	0.743
43DAP/42DAP	1.01148	1
47DAP/43DAP	1.07253	0.776
52DAP/47DAP	1.14193	0.709
57DAP/52DAP	0.89215	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59217	0.188
17DAP/reference	1.57217	0.044
27DAP/reference	2.97449	0.008
39DAP/reference	1.26322	0.144
41DAP/reference	1.27116	0.067
42DAP/reference	1.7992	0.001
43DAP/reference	1.55792	0.008
47DAP/reference	1.57727	0.071
52DAP/reference	1.0343	1
57DAP/reference	1.18985	0.582

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07098	0.34
27DAP/17DAP	0.97079	0.878
39DAP/27DAP	0.93435	0.239
41DAP/39DAP	1.00587	0.914
42DAP/41DAP	0.88819	0.241
43DAP/42DAP	1.05472	0.554
47DAP/43DAP	0.96027	0.764
52DAP/47DAP	0.95062	0.807
57DAP/52DAP	1.02254	1
57DAP/7DAP	0.94419	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02964	0.894
17DAP/reference	0.86237	0.094
27DAP/reference	0.58824	0.012
39DAP/reference	0.40131	0.011
41DAP/reference	0.39559	0.014
42DAP/reference	0.34373	0.01
43DAP/reference	0.26883	0.008
47DAP/reference	0.62343	0.128
52DAP/reference	0.3634	0.012
57DAP/reference	0.3407	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48038	0.484
17DAP/reference	2.80891	0.007
27DAP/reference	1.10634	1
39DAP/reference	0.77655	0.102
41DAP/reference	0.95237	0.441
42DAP/reference	1.62073	0.008
43DAP/reference	0.8263	0.196
47DAP/reference	1.15833	0.603
52DAP/reference	0.75004	0.037
57DAP/reference	0.73651	0.073

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81126	0.016
17DAP/reference	2.0976	0.072
27DAP/reference	1.36869	0.067
39DAP/reference	0.94417	0.328
41DAP/reference	0.811	0.167
42DAP/reference	0.67807	0.087
43DAP/reference	0.97129	0.281
47DAP/reference	1.27539	0.013
52DAP/reference	0.37233	0.047
57DAP/reference	1.78463	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.54222	0.52
26DAP/20DAP	0.96673	1
34DAP/26DAP	1.14785	0.819
51DAP/34DAP	1.15246	0.429
52DAP/51DAP	1.07924	0.662
53DAP/52DAP	0.92797	0.489
55DAP/53DAP	1.0398	0.848
57DAP/55DAP	0.88617	0.508
62DAP/57DAP	0.80968	0.466
68DAP/62DAP	1.06517	0.936
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01148	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	16.9015	0.058
Mature Green Tomato/Ripe Tomato	0.8144	0.347
Immature Eggplant/Mature Eggplant	1.0343	0.407
Ripe Pepper/Ripe Tomato	2.62987
Mature Eggplant/Ripe Tomato	4.32899	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89519	0.536
1-1-2/M82	0.70025
12-2/M82	N/A	N/A
12-4/M82	0.96123	1
1-3/M82	0.88699	1
2-1-1/M82	0.94654
2-1/M82	N/A	N/A
2-6/M82	0.73861
3-2/M82	1.04518
4-1-1/M82	0.88893	1
4-1/M82	1.9358
4-3-2/M82	N/A	N/A
4-3/M82	0.71495
5-3/M82	1.18877	1
6-2/M82	0.74367	0.481
6-3/M82	0.97446
7-1/M82	N/A	N/A
7-2/M82	0.8073	0.553
9-3-2/M82	0.91067	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.69817	0.277
IL2-6/WTpooled	1.53087	0.584
IL7-5/WTpooled	2.32824	1
IL7-3/WTpooled	0.66381	0.298
IL12-4/WTpooled	0.99004	1
IL1-4/WTpooled	0.96491	1
WT/WTpooled	0.94819	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	1.20402	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89583	1
DC3000/delta hrp 6h	1.12447	1
DC3000/delta hrp 12h	1.19426	1
DC3000/delta hrp 24h	0.99363	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.74316	0.027
DC3000 delta B/DC3000 delta AB	0.84446	0.031

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02665	1
Exp 36h	0.71303	0.539
Exp 60h	0.53237	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97995	1
Var 0h	0.50296	1
Var 12h I row2-row1	0.93503	0.363
Var 12h NI row2-row1	0.90245	0.403
Var 36h I row2-row1	0.88936	1
Var 36h NI row2-row1	1.096	0.482
Var 60h I row2-row1	1.02152	1
Var 60h NI row2-row1	0.99932	1
Time course 0hI-0hNI	0.97209	0.87
Time course 12hI-12hNI	1.02379	0.777
Time course 36hI-36hNI	1.13564	0.19
Time course 60hI-60hNI	0.58491	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)	0.65955	0.314
transgenic ySAMdc/azygous control (breaker)	2.07309	0.165
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.69921	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.19641	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.01012	0.083
Manapal/WT (break)	3.5369	0.183
Manapal/WT (red)	2.27296	0.15