Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.1.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.54121	0.019
27DAP/17DAP	1.00589	0.932
39DAP/27DAP	0.9055	0.594
41DAP/39DAP	0.85486	0.47
42DAP/41DAP	0.83962	1
43DAP/42DAP	0.92647	0.877
47DAP/43DAP	0.91067	0.591
52DAP/47DAP	1.17233	0.96
57DAP/52DAP	0.93581	0.908

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30615	0.043
17DAP/reference	0.97835	0.777
27DAP/reference	1.11693	0.264
39DAP/reference	1.1976	0.174
41DAP/reference	1.07918	0.552
42DAP/reference	0.94585	0.134
43DAP/reference	1.14844	0.042
47DAP/reference	1.25574	0.005
52DAP/reference	1.16656	0.663
57DAP/reference	1.106	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.58316	0.025
27DAP/17DAP	1.26951	0.328
39DAP/27DAP	0.61471	0.046
41DAP/39DAP	1.67807	0.579
42DAP/41DAP	1.00097	0.876
43DAP/42DAP	0.9589	0.684
47DAP/43DAP	1.05803	0.914
52DAP/47DAP	0.79581	0.226
57DAP/52DAP	1.33215	0.442
57DAP/7DAP	1.60692	0.203

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93628	0.203
17DAP/reference	1.18284	0.123
27DAP/reference	1.15683	0.008
39DAP/reference	1.01295	1
41DAP/reference	1.0138	1
42DAP/reference	1.04974	0.686
43DAP/reference	0.93686	0.305
47DAP/reference	0.93186	0.504
52DAP/reference	0.96688	0.477
57DAP/reference	1.12547	0.268

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28798	0.226
17DAP/reference	1.02272	0.674
27DAP/reference	0.97027	0.519
39DAP/reference	0.91578	0.314
41DAP/reference	0.98412	0.519
42DAP/reference	0.98157	0.594
43DAP/reference	1.31448	0.226
47DAP/reference	1.01436	1
52DAP/reference	0.9404	0.619
57DAP/reference	1.01431	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10621	0.237
17DAP/reference	1.12249	0.563
27DAP/reference	1.32206	0.067
39DAP/reference	1.20926	0.075
41DAP/reference	1.04532	1
42DAP/reference	1.10619	0.171
43DAP/reference	0.94601	0.384
47DAP/reference	1.17753	0.089
52DAP/reference	1.20935	0.759
57DAP/reference	1.36249	0.147

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14223	0.966
26DAP/20DAP	1.48286	0.165
34DAP/26DAP	0.96055	0.94
51DAP/34DAP	0.75028	0.18
52DAP/51DAP	1.15838	0.704
53DAP/52DAP	1.1584	0.413
55DAP/53DAP	1.16079	0.153
57DAP/55DAP	0.82605	0.375
62DAP/57DAP	0.91828
68DAP/62DAP	0.61478	0.579
68DAP/14DAP	0.83451	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	N/A	N/A

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.71526	0.058
Mature Green Tomato/Ripe Tomato	2.41789	0.02
Immature Eggplant/Mature Eggplant	0.86059	0.329
Ripe Pepper/Ripe Tomato	0.99803	1
Mature Eggplant/Ripe Tomato	5.04773	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.61868
12-2/M82	N/A	N/A
12-4/M82	0.56306	0.319
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	N/A	N/A
5-3/M82	0.93276	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.04559
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.76188	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.23619
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.27937
IL1-4/WTpooled	1.41714	1
WT/WTpooled	0.989	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	0.72914	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89657	1
DC3000/delta hrp 6h	1.32187	1
DC3000/delta hrp 12h	1.02661	1
DC3000/delta hrp 24h	0.61961	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64885	0.023
DC3000 delta B/DC3000 delta AB	0.64559	0.121

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06598	1
Exp 36h	0.87401	0.589
Exp 60h	0.79226	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93417	1
Var 0h	1.19669	0.98
Var 12h I row2-row1	0.82053	0.467
Var 12h NI row2-row1	1.20927	0.649
Var 36h I row2-row1	0.99641	1
Var 36h NI row2-row1	1.58171	1
Var 60h I row2-row1	1.10624	1
Var 60h NI row2-row1	1.16814	0.904
Time course 0hI-0hNI	3.12287	0.833
Time course 12hI-12hNI	0.8317	0.055
Time course 36hI-36hNI	0.66037	0.023
Time course 60hI-60hNI	0.11575	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)	1.13915	0.232
transgenic ySAMdc/azygous control (breaker)	0.91464	0.173
transgenic ySAMdc/azygous control (red)	1.65661	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08303	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.27001	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.34288	0.084
Manapal/WT (break)	2.88977	0.13
Manapal/WT (red)	3.64099	0.142