Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.1.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88411	0.464
27DAP/17DAP	0.64507	0.065
39DAP/27DAP	0.70219	0.402
41DAP/39DAP	0.89871	0.607
42DAP/41DAP	1.07721	0.92
43DAP/42DAP	1.1907	0.985
47DAP/43DAP	0.83707	0.496
52DAP/47DAP	0.75744	0.418
57DAP/52DAP	0.8653	0.71

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81021	0.049
17DAP/reference	0.67589	0.007
27DAP/reference	0.71059	0.014
39DAP/reference	0.80897	0.014
41DAP/reference	0.69869	0.016
42DAP/reference	0.81292	0.012
43DAP/reference	0.68122	0.013
47DAP/reference	0.74703	0.001
52DAP/reference	0.63536	0.013
57DAP/reference	0.76782	0.036

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28875	0.201
27DAP/17DAP	0.76299	0.295
39DAP/27DAP	0.62236	0.04
41DAP/39DAP	1.05614	0.883
42DAP/41DAP	0.94902	0.637
43DAP/42DAP	1.03153	0.746
47DAP/43DAP	1.01511	0.973
52DAP/47DAP	1.06203	0.835
57DAP/52DAP	0.8387	0.366
57DAP/7DAP	1.03506

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90272	0.168
17DAP/reference	0.73668	0.049
27DAP/reference	0.76479	0.024
39DAP/reference	0.48543	0.011
41DAP/reference	0.58871	0.031
42DAP/reference	0.56056	0.01
43DAP/reference	0.36251	0.009
47DAP/reference	0.68424	0.128
52DAP/reference	0.43439	0.01
57DAP/reference	0.3732	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75346	0.041
17DAP/reference	0.78871	0.08
27DAP/reference	0.7377	0.039
39DAP/reference	0.63485	0.01
41DAP/reference	0.80544	0.028
42DAP/reference	0.85011	0.073
43DAP/reference	0.62207	0.005
47DAP/reference	0.85504	0.099
52DAP/reference	0.60357	0.003
57DAP/reference	0.56456	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53347	0.022
17DAP/reference	1.67843	0.113
27DAP/reference	1.15101	0.248
39DAP/reference	0.99497	0.755
41DAP/reference	1.05898	0.56
42DAP/reference	0.96429	0.552
43DAP/reference	0.96487	0.614
47DAP/reference	0.96649	0.465
52DAP/reference	0.72929	0.066
57DAP/reference	1.19739	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05951	0.966
26DAP/20DAP	1.06682	1
34DAP/26DAP	0.94303	0.857
51DAP/34DAP	1.01217	1
52DAP/51DAP	0.78948	1
53DAP/52DAP	0.68874	0.074
55DAP/53DAP	0.73999	0.21
57DAP/55DAP	1.14608	0.854
62DAP/57DAP	0.8201	0.28
68DAP/62DAP	1.0565	0.863
68DAP/14DAP	1.44602	0.328

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.53132	0.032

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09423	0.176
Mature Green Tomato/Ripe Tomato	0.78001	0.086
Immature Eggplant/Mature Eggplant	0.5248	0.058
Ripe Pepper/Ripe Tomato	1.33813	1
Mature Eggplant/Ripe Tomato	1.0819	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.47157	0.591
1-1-2/M82	1.20944	1
12-2/M82	0.69827	0.678
12-4/M82	1.11667	1
1-3/M82	1.16019	1
2-1-1/M82	1.17216	0.403
2-1/M82	0.86828
2-6/M82	1.00881	1
3-2/M82	1.25689	0.967
4-1-1/M82	1.10742	1
4-1/M82	N/A	N/A
4-3-2/M82	1.63286	0.284
4-3/M82	1.98396	0.268
5-3/M82	0.98614	1
6-2/M82	0.65373	0.497
6-3/M82	N/A	N/A
7-1/M82	1.17102
7-2/M82	0.80719	0.881
9-3-2/M82	1.06826	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63641	0.243
IL2-6/WTpooled	1.03525	1
IL7-5/WTpooled	0.8471	1
IL7-3/WTpooled	0.83239	1
IL12-4/WTpooled	1.05458	0.891
IL1-4/WTpooled	0.88517	0.699
WT/WTpooled	0.96451	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	1.04287	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93654
DC3000/delta hrp 6h	0.89966	0.95
DC3000/delta hrp 12h	1.12978	1
DC3000/delta hrp 24h	0.80428	0.047

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.6422	0.045
DC3000 delta B/DC3000 delta AB	0.43245	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01857	1
Exp 36h	0.87879	0.699
Exp 60h	0.87235	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96017	1
Var 0h	0.65582	0.933
Var 12h I row2-row1	0.92901	0.77
Var 12h NI row2-row1	1.02224	1
Var 36h I row2-row1	0.88332	1
Var 36h NI row2-row1	0.95747	0.743
Var 60h I row2-row1	1.44327	0.562
Var 60h NI row2-row1	0.97826	1
Time course 0hI-0hNI	1.00467	1
Time course 12hI-12hNI	1.04192	0.811
Time course 36hI-36hNI	1.01693	0.881
Time course 60hI-60hNI	0.3214	0.009

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)	0.9563	0.377
transgenic ySAMdc/azygous control (breaker)	1.27345	0.178
transgenic ySAMdc/azygous control (red)	1.21208	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.76284	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.61277	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.58543	0.105
Manapal/WT (break)	1.54589	0.183
Manapal/WT (red)	1.20049	0.222