Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10171	0.838
27DAP/17DAP	0.96563	0.978
39DAP/27DAP	1.27034	0.685
41DAP/39DAP	1.40155	0.597
42DAP/41DAP	0.9202	1
43DAP/42DAP	0.69101	0.454
47DAP/43DAP	0.97544	0.84
52DAP/47DAP	0.90418	0.651
57DAP/52DAP	0.94378	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0052	0.824
17DAP/reference	0.91655	0.158
27DAP/reference	0.92492	0.215
39DAP/reference	0.98812	0.841
41DAP/reference	0.94082	0.341
42DAP/reference	1.00892	1
43DAP/reference	0.85293	0.02
47DAP/reference	0.95664	0.242
52DAP/reference	1.18394	0.096
57DAP/reference	1.12217	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83986	0.07
27DAP/17DAP	0.9668	0.887
39DAP/27DAP	1.03597	0.811
41DAP/39DAP	1.14625	0.735
42DAP/41DAP	0.87254	0.548
43DAP/42DAP	1.06569	0.25
47DAP/43DAP	1.03383	0.973
52DAP/47DAP	0.97476	0.917
57DAP/52DAP	0.97143	0.73
57DAP/7DAP	1.78806

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85026	0.146
17DAP/reference	1.00877	1
27DAP/reference	0.99346	0.656
39DAP/reference	0.75146	0.011
41DAP/reference	0.89278	0.116
42DAP/reference	0.89697	0.09
43DAP/reference	0.84062	0.02
47DAP/reference	0.84911	0.128
52DAP/reference	0.93489	0.15
57DAP/reference	0.92405	0.207

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98422	0.77
17DAP/reference	1.21173	0.127
27DAP/reference	1.09925	0.497
39DAP/reference	1.01549	0.722
41DAP/reference	1.02148	1
42DAP/reference	1.25887	0.039
43DAP/reference	1.57908	0.116
47DAP/reference	1.0698	0.095
52DAP/reference	0.94034	0.171
57DAP/reference	0.99879	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95949	0.455
17DAP/reference	1.15923	0.531
27DAP/reference	0.92623	0.062
39DAP/reference	1.08491	0.377
41DAP/reference	1.14043	0.319
42DAP/reference	1.14038	0.481
43DAP/reference	1.26706	0.157
47DAP/reference	1.00074	0.687
52DAP/reference	0.91655	0.395
57DAP/reference	1.40562	0.085

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01238	1
26DAP/20DAP	1.01854	1
34DAP/26DAP	1.6617	0.819
51DAP/34DAP	0.93497	0.785
52DAP/51DAP	0.77771	1
53DAP/52DAP	1.11365	1
55DAP/53DAP	0.75495	0.203
57DAP/55DAP	1.05609	0.961
62DAP/57DAP	0.88549	0.466
68DAP/62DAP	1.12993	0.899
68DAP/14DAP	1.6933	0.436

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18099	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.21456	0.073
Mature Green Tomato/Ripe Tomato	1.19092	0.437
Immature Eggplant/Mature Eggplant	2.27831	0.05
Ripe Pepper/Ripe Tomato	1.24069
Mature Eggplant/Ripe Tomato	1.07555

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10908	0.742
1-1-2/M82	0.70149
12-2/M82	1.49199
12-4/M82	1.27663
1-3/M82	N/A	N/A
2-1-1/M82	0.80215
2-1/M82	N/A	N/A
2-6/M82	0.83712	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.59641
4-1/M82	1.18813
4-3-2/M82	1.08149
4-3/M82	N/A	N/A
5-3/M82	1.23476
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.06092
7-2/M82	0.77583
9-3-2/M82	1.1689

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.54248	0.247
IL2-6/WTpooled	0.73053	0.473
IL7-5/WTpooled	0.89875	1
IL7-3/WTpooled	0.97375	1
IL12-4/WTpooled	0.5783	0.497
IL1-4/WTpooled	0.6867	0.444
WT/WTpooled	1.09315	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	1.07023	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98409	1
DC3000/delta hrp 6h	0.92555	0.95
DC3000/delta hrp 12h	1.10017	1
DC3000/delta hrp 24h	0.93163	0.483

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88777
DC3000 delta B/DC3000 delta AB	1.22836	0.327

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04749	1
Exp 36h	1.48798	1
Exp 60h	1.94162	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00962	1
Var 0h	1.29843	0.98
Var 12h I row2-row1	1.16244	0.613
Var 12h NI row2-row1	0.99781	1
Var 36h I row2-row1	0.87798	1
Var 36h NI row2-row1	0.91777	0.743
Var 60h I row2-row1	0.72564	0.439
Var 60h NI row2-row1	1.30667	0.904
Time course 0hI-0hNI	1.14349	0.486
Time course 12hI-12hNI	1.12315	0.398
Time course 36hI-36hNI	1.28893	0.063
Time course 60hI-60hNI	2.93237	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)	0.73482	0.301
transgenic ySAMdc/azygous control (breaker)	0.96513	0.173
transgenic ySAMdc/azygous control (red)	0.87208	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.92365	0.06

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26301	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.25112	0.307
Manapal/WT (break)	0.81807	1
Manapal/WT (red)	0.58622	0.181