Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.13.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10113	0.863
27DAP/17DAP	1.21184	0.813
39DAP/27DAP	1.02973	0.82
41DAP/39DAP	1.42941	0.342
42DAP/41DAP	1.4615	0.519
43DAP/42DAP	0.77772	0.467
47DAP/43DAP	0.96707	0.729
52DAP/47DAP	1.70913	0.333
57DAP/52DAP	0.82697	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98633	0.63
17DAP/reference	1.06389	0.051
27DAP/reference	0.95847	0.497
39DAP/reference	1.01316	0.786
41DAP/reference	1.11657	0.158
42DAP/reference	0.94231	0.151
43DAP/reference	1.13825	0.031
47DAP/reference	0.92885	0.137
52DAP/reference	0.79197	0.093
57DAP/reference	0.81301	0.054

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93982	0.542
27DAP/17DAP	1.00154	0.943
39DAP/27DAP	0.9995	0.997
41DAP/39DAP	1.22251	0.705
42DAP/41DAP	1.03238	0.936
43DAP/42DAP	1.04362	0.699
47DAP/43DAP	1.12989	0.699
52DAP/47DAP	0.93538	0.763
57DAP/52DAP	0.9669	0.7
57DAP/7DAP	1.61158	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80933	0.1
17DAP/reference	0.92514	0.094
27DAP/reference	0.95358	0.171
39DAP/reference	0.96601	0.411
41DAP/reference	0.95594	0.298
42DAP/reference	0.96867	0.211
43DAP/reference	0.91817	0.047
47DAP/reference	0.98702	0.671
52DAP/reference	0.90731	0.053
57DAP/reference	0.92265	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13548	0.241
17DAP/reference	1.00484	0.805
27DAP/reference	0.77228	0.069
39DAP/reference	0.79695	0.159
41DAP/reference	0.82536	0.091
42DAP/reference	0.85354	0.135
43DAP/reference	1.17021	0.195
47DAP/reference	0.9959	0.695
52DAP/reference	0.95539	0.351
57DAP/reference	1.44683	0.091

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97829	0.29
17DAP/reference	1.05718	0.685
27DAP/reference	1.02229	0.575
39DAP/reference	0.95226	0.299
41DAP/reference	0.93314	0.209
42DAP/reference	0.77037	0.134
43DAP/reference	0.79539	0.131
47DAP/reference	1.06745	0.82
52DAP/reference	0.86069	0.164
57DAP/reference	0.56687	0.042

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33449	0.966
26DAP/20DAP	0.93915	1
34DAP/26DAP	1.16227	0.154
51DAP/34DAP	0.92288	0.611
52DAP/51DAP	1.18188	0.213
53DAP/52DAP	1.02644	0.901
55DAP/53DAP	1.04868	0.922
57DAP/55DAP	1.09694	0.793
62DAP/57DAP	1.32741	0.115
68DAP/62DAP	0.82997	0.406
68DAP/14DAP	0.4243	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98185	0.665

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.63082	0.02
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.17556	1
Mature Eggplant/Ripe Tomato	0.05212

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99561	1
1-1-2/M82	0.88039	1
12-2/M82	1.06753
12-4/M82	0.84874	1
1-3/M82	0.77067	0.378
2-1-1/M82	0.87597	0.92
2-1/M82	N/A	N/A
2-6/M82	1.1324	0.594
3-2/M82	N/A	N/A
4-1-1/M82	0.97041	1
4-1/M82	0.87984	1
4-3-2/M82	0.92928	1
4-3/M82	0.74016
5-3/M82	0.8888	1
6-2/M82	0.86847
6-3/M82	0.88865
7-1/M82	1.01241	1
7-2/M82	0.93001	0.881
9-3-2/M82	1.11962	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.27436	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83046	0.294
IL12-4/WTpooled	1.14966	0.839
IL1-4/WTpooled	0.92659	1
WT/WTpooled	0.99899	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	1.28593	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95007	1
DC3000/delta hrp 6h	0.97265	0.95
DC3000/delta hrp 12h	1.00572	1
DC3000/delta hrp 24h	1.03548	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.60237	0.022
DC3000 delta B/DC3000 delta AB	1.6318	0.141

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.272	1
Exp 36h	1.76106	0.489
Exp 60h	1.98521	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00316	1
Var 0h	1.03533	0.98
Var 12h I row2-row1	1.12186	0.473
Var 12h NI row2-row1	0.92801	0.627
Var 36h I row2-row1	1.07888	0.908
Var 36h NI row2-row1	0.82334	0.522
Var 60h I row2-row1	0.84903	0.439
Var 60h NI row2-row1	0.90269	0.866
Time course 0hI-0hNI	1.11364	0.719
Time course 12hI-12hNI	1.54912	0.008
Time course 36hI-36hNI	2.3807	0.005
Time course 60hI-60hNI	4.35981	0.008

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)	1.36432	0.748
transgenic ySAMdc/azygous control (breaker)	0.64099	0.251
transgenic ySAMdc/azygous control (red)	1.61461	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0183	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.06437	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.78336	0.084
Manapal/WT (break)	0.97944	1
Manapal/WT (red)	0.8567	0.503