Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.05541	0.05
27DAP/17DAP	1.50612	0.677
39DAP/27DAP	1.2317	0.603
41DAP/39DAP	0.89176	0.563
42DAP/41DAP	1.05162	1
43DAP/42DAP	1.46824	0.453
47DAP/43DAP	1.09342	0.756
52DAP/47DAP	0.66345	0.23
57DAP/52DAP	1.28156	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88869	0.277
17DAP/reference	0.82408	0.079
27DAP/reference	0.86639	0.17
39DAP/reference	0.94243	0.565
41DAP/reference	0.86342	0.267
42DAP/reference	0.86463	0.078
43DAP/reference	0.8931	0.222
47DAP/reference	0.81623	0.025
52DAP/reference	1.03316	1
57DAP/reference	0.91745	0.124

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.9127	0.036
27DAP/17DAP	1.34998	0.042
39DAP/27DAP	1.13896	0.219
41DAP/39DAP	1.27843	0.59
42DAP/41DAP	0.91885	0.499
43DAP/42DAP	1.31719	0.038
47DAP/43DAP	1.10381	0.3
52DAP/47DAP	1.1749	0.66
57DAP/52DAP	0.69493	0.092
57DAP/7DAP	1.77466	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0744	0.576
17DAP/reference	0.97677	0.518
27DAP/reference	1.15743	0.088
39DAP/reference	0.96855	0.411
41DAP/reference	1.31863	0.02
42DAP/reference	1.34792	0.046
43DAP/reference	1.17491	0.124
47DAP/reference	1.11364	0.571
52DAP/reference	1.13355	0.266
57DAP/reference	0.86595	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89796	0.353
17DAP/reference	0.86416	0.164
27DAP/reference	0.98078	0.576
39DAP/reference	1.03039	0.603
41DAP/reference	0.98232	0.481
42DAP/reference	1.17719	0.17
43DAP/reference	1.15932	0.347
47DAP/reference	1.17727	0.138
52DAP/reference	0.80135	0.203
57DAP/reference	1.16737	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11245	0.18
17DAP/reference	1.1259	0.563
27DAP/reference	1.32011	0.038
39DAP/reference	1.24603	0.025
41DAP/reference	1.32211	0.016
42DAP/reference	1.17137	0.529
43DAP/reference	0.96648	0.523
47DAP/reference	0.7874	0.093
52DAP/reference	1.01002	0.908
57DAP/reference	0.70274	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14611	0.966
26DAP/20DAP	1.161	0.409
34DAP/26DAP	0.9449	0.874
51DAP/34DAP	0.81886	0.333
52DAP/51DAP	0.90188	1
53DAP/52DAP	1.18754	0.806
55DAP/53DAP	1.46189	0.079
57DAP/55DAP	0.78865	0.219
62DAP/57DAP	0.85095	0.681
68DAP/62DAP	1.10803	0.872
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.58207	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.01865	1
Mature Green Tomato/Ripe Tomato	1.35805	0.523
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	6.02865
Mature Eggplant/Ripe Tomato	1.10078

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95048	0.944
1-1-2/M82	1.00712	1
12-2/M82	0.915
12-4/M82	1.22159	1
1-3/M82	0.94645	1
2-1-1/M82	1.13622	0.764
2-1/M82	0.829
2-6/M82	1.04094	1
3-2/M82	0.83417
4-1-1/M82	0.94057	0.985
4-1/M82	0.84827	0.69
4-3-2/M82	0.52456	0.487
4-3/M82	0.83554	0.72
5-3/M82	0.86195	0.642
6-2/M82	1.0448	1
6-3/M82	1.37141
7-1/M82	0.88042
7-2/M82	1.15481	0.324
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	0.99365	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10577	1
IL12-4/WTpooled	1.11645	0.624
IL1-4/WTpooled	1.09932
WT/WTpooled	0.9901	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	1.1664	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03523	0.921
DC3000/delta hrp 6h	0.72476	0.757
DC3000/delta hrp 12h	1.10709	1
DC3000/delta hrp 24h	1.15928	0.174

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50695
DC3000 delta B/DC3000 delta AB	0.75211	0.039

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5261	1
Exp 36h	1.80472	0.489
Exp 60h	2.4767	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94288	1
Var 0h	0.58168	0.933
Var 12h I row2-row1	0.86673	0.338
Var 12h NI row2-row1	1.112	0.649
Var 36h I row2-row1	1.06133	0.601
Var 36h NI row2-row1	0.91708	0.743
Var 60h I row2-row1	1.10692	0.562
Var 60h NI row2-row1	0.89339	0.458
Time course 0hI-0hNI	1.05316	0.764
Time course 12hI-12hNI	0.96515	0.802
Time course 36hI-36hNI	1.14497	0.19
Time course 60hI-60hNI	1.11051	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)	1.04275	0.748
transgenic ySAMdc/azygous control (breaker)	1.0401	1
transgenic ySAMdc/azygous control (red)	0.80975	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99743	0.886

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40372	0.238

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)	N/A	N/A
Manapal/WT (red)	0.8809	0.728