Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.79209	0.042
27DAP/17DAP	1.60319	0.3
39DAP/27DAP	1.15861	0.732
41DAP/39DAP	0.70082	0.141
42DAP/41DAP	1.08216	0.938
43DAP/42DAP	0.91305	0.807
47DAP/43DAP	1.74737	0.253
52DAP/47DAP	0.68706	0.262
57DAP/52DAP	0.70487	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79009	0.063
17DAP/reference	0.91985	0.342
27DAP/reference	1.372	0.022
39DAP/reference	1.29569	0.083
41DAP/reference	1.18129	0.041
42DAP/reference	1.57173	0.001
43DAP/reference	1.5694	0.011
47DAP/reference	2.15683	0.001
52DAP/reference	1.43105	0.01
57DAP/reference	1.49276	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.72247	0.041
27DAP/17DAP	0.9437	0.58
39DAP/27DAP	1.13109	0.285
41DAP/39DAP	1.00407	0.986
42DAP/41DAP	1.24888	0.006
43DAP/42DAP	1.08443	0.192
47DAP/43DAP	0.91393	0.145
52DAP/47DAP	1.10154	0.756
57DAP/52DAP	1.12971	0.662
57DAP/7DAP	1.77823	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.16101	0.036
17DAP/reference	4.61788	0.006
27DAP/reference	5.80741	0.006
39DAP/reference	6.55147	0.005
41DAP/reference	5.58351	0.011
42DAP/reference	9.6979	0.006
43DAP/reference	8.82435	0.006
47DAP/reference	6.52068	0.014
52DAP/reference	7.54826	0.007
57DAP/reference	6.01053	0.003

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94944	0.412
17DAP/reference	1.06497	0.773
27DAP/reference	1.43951	0.033
39DAP/reference	1.58665	0.011
41DAP/reference	1.64265	0.005
42DAP/reference	1.37926	0.011
43DAP/reference	1.29206	0.569
47DAP/reference	1.64697	0.008
52DAP/reference	1.26512	0.015
57DAP/reference	1.07385	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.11583	0.098
17DAP/reference	2.13468	0.456
27DAP/reference	5.02213	0.016
39DAP/reference	5.76571	0.007
41DAP/reference	5.80959	0.006
42DAP/reference	5.38833	0.011
43DAP/reference	5.37909	0.008
47DAP/reference	2.23369	0.008
52DAP/reference	5.40749	0.029
57DAP/reference	4.12217	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35992	0.966
26DAP/20DAP	1.14469	0.604
34DAP/26DAP	0.97204	1
51DAP/34DAP	1.10137	0.917
52DAP/51DAP	1.1516	0.579
53DAP/52DAP	1.00815	0.983
55DAP/53DAP	1.0857	0.712
57DAP/55DAP	1.11528	0.906
62DAP/57DAP	0.90339	0.088
68DAP/62DAP	1.31802	0.23
68DAP/14DAP	1.31678	0.057

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.61432	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.98061	0.805
Mature Green Tomato/Ripe Tomato	0.97085	0.66
Immature Eggplant/Mature Eggplant	1.07032	0.278
Ripe Pepper/Ripe Tomato	0.32001	0.224
Mature Eggplant/Ripe Tomato	0.44437	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89057	0.944
1-1-2/M82	1.37915	1
12-2/M82	1.01181	1
12-4/M82	1.11086	1
1-3/M82	1.81857	0.277
2-1-1/M82	0.97049	1
2-1/M82	0.75307	0.74
2-6/M82	0.45427	1
3-2/M82	1.27172	0.84
4-1-1/M82	1.4188	0.968
4-1/M82	1.37615	1
4-3-2/M82	1.29587	0.508
4-3/M82	0.9802	1
5-3/M82	0.98218	1
6-2/M82	1.03626	1
6-3/M82	0.99095	1
7-1/M82	1.08983	0.925
7-2/M82	1.00281	1
9-3-2/M82	0.96815	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89692	0.247
IL2-6/WTpooled	1.00175	1
IL7-5/WTpooled	0.99465	1
IL7-3/WTpooled	1.06007	1
IL12-4/WTpooled	0.89382	0.71
IL1-4/WTpooled	1.03649	1
WT/WTpooled	0.90612	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	1.11967	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90419	0.941
DC3000/delta hrp 6h	1.08688	1
DC3000/delta hrp 12h	0.96656	1
DC3000/delta hrp 24h	0.54996	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10289	0.27
DC3000 delta B/DC3000 delta AB	0.92969	0.674

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.13514	1
Exp 36h	0.95301	0.879
Exp 60h	1.03867	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98922	1
Var 0h	0.99817	1
Var 12h I row2-row1	0.95596	0.467
Var 12h NI row2-row1	0.88565	0.546
Var 36h I row2-row1	1.09104	1
Var 36h NI row2-row1	1.02824	1
Var 60h I row2-row1	0.9407	0.582
Var 60h NI row2-row1	0.90855	0.756
Time course 0hI-0hNI	1.03658	0.833
Time course 12hI-12hNI	1.06955	0.373
Time course 36hI-36hNI	1.00199	1
Time course 60hI-60hNI	0.86737	0.081

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)	0.72351	0.291
transgenic ySAMdc/azygous control (breaker)	0.56607	0.125
transgenic ySAMdc/azygous control (red)	1.0243	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.09574	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84785	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01916	1
Manapal/WT (break)	0.84314	1
Manapal/WT (red)	0.97579	0.863