Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.9.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29785	0.575
27DAP/17DAP	1.8918	0.646
39DAP/27DAP	0.91569	0.594
41DAP/39DAP	0.9328	0.807
42DAP/41DAP	0.94975	1
43DAP/42DAP	0.91551	0.822
47DAP/43DAP	1.11007	0.965
52DAP/47DAP	1.0215	0.982
57DAP/52DAP	2.13768	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03771	0.872
17DAP/reference	1.22658	0.022
27DAP/reference	1.03492	0.612
39DAP/reference	0.88753	0.221
41DAP/reference	1.14787	0.015
42DAP/reference	0.92726	0.139
43DAP/reference	1.05907	0.646
47DAP/reference	0.98021	0.445
52DAP/reference	0.86424	0.108
57DAP/reference	1.0417	0.6

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65359	0.036
27DAP/17DAP	0.99173	0.943
39DAP/27DAP	0.94445	0.579
41DAP/39DAP	1.21619	0.06
42DAP/41DAP	0.92639	0.491
43DAP/42DAP	0.70174	0.022
47DAP/43DAP	1.04609	0.833
52DAP/47DAP	1.02769	0.927
57DAP/52DAP	1.25216	0.325
57DAP/7DAP	1.3534	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99828	0.758
17DAP/reference	1.06798	0.525
27DAP/reference	1.11459	0.16
39DAP/reference	1.16362	0.486
41DAP/reference	0.82563	0.032
42DAP/reference	0.76342	0.06
43DAP/reference	1.09536	0.537
47DAP/reference	1.09047	0.595
52DAP/reference	1.25566	0.171
57DAP/reference	1.45082	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10082	0.538
17DAP/reference	1.27988	0.098
27DAP/reference	1.23018	0.239
39DAP/reference	1.07862	0.67
41DAP/reference	1.0239	0.666
42DAP/reference	1.02932	1
43DAP/reference	1.25418	0.087
47DAP/reference	1.07666	0.544
52DAP/reference	1.11617	0.368
57DAP/reference	1.14971	0.334

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04083	0.827
17DAP/reference	0.97673	0.658
27DAP/reference	0.98524	0.624
39DAP/reference	0.95073	0.328
41DAP/reference	0.85249	0.185
42DAP/reference	1.03306	1
43DAP/reference	0.90107	0.256
47DAP/reference	1.04219	0.934
52DAP/reference	1.20448	0.566
57DAP/reference	0.91039	0.184

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18142	0.966
26DAP/20DAP	1.12481	1
34DAP/26DAP	0.64726	0.109
51DAP/34DAP	1.21566	0.303
52DAP/51DAP	0.85207	1
53DAP/52DAP	1.04547	0.935
55DAP/53DAP	1.09418	0.876
57DAP/55DAP	1.02502	0.975
62DAP/57DAP	0.80465	0.28
68DAP/62DAP	1.45703	0.113
68DAP/14DAP	0.87563	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.54034	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.22975	0.523
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.982
Mature Eggplant/Ripe Tomato	0.57773	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.61513	0.503
1-1-2/M82	0.41773
12-2/M82	0.94899	1
12-4/M82	0.81969	0.358
1-3/M82	1.33989
2-1-1/M82	1.11381
2-1/M82	0.78304
2-6/M82	0.97471
3-2/M82	1.4133
4-1-1/M82	1.18845	0.977
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.99512	1
5-3/M82	1.17362	0.496
6-2/M82	0.93141
6-3/M82	0.98715	1
7-1/M82	1.18081	0.556
7-2/M82	1.00927
9-3-2/M82	N/A	N/A

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	0.9538	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.34728	0.921
DC3000/delta hrp 6h	1.93434	1
DC3000/delta hrp 12h	0.96791	1
DC3000/delta hrp 24h	1.10408	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02762	1
Exp 36h	1.03403	0.489
Exp 60h	1.28651	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04109	1
Var 0h	3.039	0.936
Var 12h I row2-row1	1.16109	0.544
Var 12h NI row2-row1	1.22147	0.34
Var 36h I row2-row1	0.93973	1
Var 36h NI row2-row1	0.73988	0.421
Var 60h I row2-row1	1.25412
Var 60h NI row2-row1	0.95665	0.756
Time course 0hI-0hNI	0.93299	0.572
Time course 12hI-12hNI	0.94982	0.701
Time course 36hI-36hNI	1.25649	0.218
Time course 60hI-60hNI	0.88087	0.161

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)	0.90021	0.314
transgenic ySAMdc/azygous control (breaker)	1.29261	0.178
transgenic ySAMdc/azygous control (red)	1.01086	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96943	0.201

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72213	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79588	1
Manapal/WT (break)	0.86479	0.333
Manapal/WT (red)	1.04806	0.413