Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31762	0.325
27DAP/17DAP	1.42133	0.793
39DAP/27DAP	1.35144	0.47
41DAP/39DAP	1.27563	0.708
42DAP/41DAP	1.25313	0.404
43DAP/42DAP	1.55717	0.899
47DAP/43DAP	7.03596	0.156
52DAP/47DAP	0.77691	0.466
57DAP/52DAP	1.58857	0.837

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87156	0.14
17DAP/reference	1.20649	0.258
27DAP/reference	0.90229	0.275
39DAP/reference	1.07706	0.534
41DAP/reference	1.22018	0.111
42DAP/reference	1.08607	0.264
43DAP/reference	1.00105	0.924
47DAP/reference	1.05197	0.708
52DAP/reference	1.37803	0.025
57DAP/reference	1.10657	0.564

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45835	0.201
27DAP/17DAP	1.13999	0.798
39DAP/27DAP	0.86437	0.35
41DAP/39DAP	0.84331	0.495
42DAP/41DAP	1.15177	0.81
43DAP/42DAP	2.74889	0.014
47DAP/43DAP	1.06966	0.926
52DAP/47DAP	1.15014	0.734
57DAP/52DAP	1.03581	0.892
57DAP/7DAP	1.7581	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83714	0.104
17DAP/reference	0.82024	0.108
27DAP/reference	0.82952	0.117
39DAP/reference	0.73265	0.016
41DAP/reference	0.81176	0.033
42DAP/reference	0.71163	0.017
43DAP/reference	0.83165	0.054
47DAP/reference	0.8237	0.066
52DAP/reference	0.91377	0.196
57DAP/reference	0.77816	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84803	0.318
17DAP/reference	0.96207	0.626
27DAP/reference	0.93397	0.352
39DAP/reference	0.85542	0.087
41DAP/reference	1.00571	0.735
42DAP/reference	1.29645	0.022
43DAP/reference	0.91025	0.385
47DAP/reference	1.04669	0.841
52DAP/reference	1.08494	0.702
57DAP/reference	1.02212	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87196	0.135
17DAP/reference	1.13403	0.775
27DAP/reference	0.78284	0.027
39DAP/reference	0.93186	0.36
41DAP/reference	0.96295	0.56
42DAP/reference	0.97778	0.671
43DAP/reference	1.17943	0.241
47DAP/reference	0.93192	0.396
52DAP/reference	0.92333	0.472
57DAP/reference	1.51205	0.371

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.1419	0.966
26DAP/20DAP	1.11021
34DAP/26DAP	1.60249	0.819
51DAP/34DAP	0.28904
52DAP/51DAP	0.73672
53DAP/52DAP	1.27075	0.806
55DAP/53DAP	1.25809	0.748
57DAP/55DAP	1.0712	0.997
62DAP/57DAP	1.15349	0.868
68DAP/62DAP	1.5424	0.956
68DAP/14DAP	1.22522

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.43401	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.0609	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.21307
Mature Eggplant/Ripe Tomato	0.0253	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37481
1-1-2/M82	1.50772	1
12-2/M82	0.80436	0.955
12-4/M82	1.242	1
1-3/M82	2.13472	1
2-1-1/M82	1.27352	0.343
2-1/M82	0.9618
2-6/M82	0.75953	0.421
3-2/M82	1.60667	0.84
4-1-1/M82	0.70459
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.18265	1
5-3/M82	0.87402	1
6-2/M82	1.53383
6-3/M82	0.53327
7-1/M82	1.05218	1
7-2/M82	1.09142	0.302
9-3-2/M82	1.69304	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92609	0.321
IL2-6/WTpooled	0.86444	0.473
IL7-5/WTpooled	0.61066	1
IL7-3/WTpooled	0.89127	0.418
IL12-4/WTpooled	1.21597	0.785
IL1-4/WTpooled	1.1294	1
WT/WTpooled	1.06908	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	0.79163

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21615	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	2.23358	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.42987
DC3000 delta B/DC3000 delta AB	1.63402

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.35676	1
Var 0h	1.17824	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	1.02595	1
Var 36h I row2-row1	0.42302	1
Var 36h NI row2-row1	1.32053
Var 60h I row2-row1	1.27682	1
Var 60h NI row2-row1	1.2591
Time course 0hI-0hNI	1.40446	0.662
Time course 12hI-12hNI	0.68068	0.511
Time course 36hI-36hNI	1.64234	0.651
Time course 60hI-60hNI	1.07092	0.673

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.53644	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.83551	1
Manapal/WT (red)	1.00854	1