Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.1.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02321	0.964
27DAP/17DAP	0.95062	0.939
39DAP/27DAP	0.95954	0.682
41DAP/39DAP	1.06659	0.483
42DAP/41DAP	0.96854	1
43DAP/42DAP	1.00512	0.937
47DAP/43DAP	0.83053	0.444
52DAP/47DAP	1.10902	0.699
57DAP/52DAP	1.03645	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99224	0.707
17DAP/reference	1.09129	0.041
27DAP/reference	0.9982	0.885
39DAP/reference	1.00339	0.871
41DAP/reference	1.00626	0.91
42DAP/reference	0.95434	0.085
43DAP/reference	1.02436	0.617
47DAP/reference	0.87457	0.014
52DAP/reference	0.93409	0.371
57DAP/reference	0.90316	0.101

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03112	0.899
27DAP/17DAP	1.09795	0.621
39DAP/27DAP	0.99046	0.953
41DAP/39DAP	1.08843	0.887
42DAP/41DAP	0.98184	0.774
43DAP/42DAP	0.9505	0.558
47DAP/43DAP	1.04555	0.889
52DAP/47DAP	0.96006	0.839
57DAP/52DAP	0.97116	0.632
57DAP/7DAP	1.01307	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83061	0.091
17DAP/reference	0.71933	0.011
27DAP/reference	0.66977	0.01
39DAP/reference	0.85161	0.049
41DAP/reference	0.74797	0.015
42DAP/reference	0.67507	0.01
43DAP/reference	0.68031	0.01
47DAP/reference	0.78518	0.03
52DAP/reference	0.73927	0.026
57DAP/reference	0.76336	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99615	0.93
17DAP/reference	0.96203	0.189
27DAP/reference	0.86168	0.097
39DAP/reference	0.96747	0.428
41DAP/reference	0.81383	0.011
42DAP/reference	0.84414	0.081
43DAP/reference	0.94077	0.269
47DAP/reference	0.883	0.013
52DAP/reference	1.00548	1
57DAP/reference	1.03539	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77488	0.061
17DAP/reference	0.90579	0.305
27DAP/reference	0.84467	0.048
39DAP/reference	0.72176	0.011
41DAP/reference	0.82418	0.086
42DAP/reference	0.65638	0.014
43DAP/reference	0.75954	0.017
47DAP/reference	0.94213	0.348
52DAP/reference	0.7014	0.142
57DAP/reference	0.60518	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01737	0.966
26DAP/20DAP	1.43921	0.141
34DAP/26DAP	0.98257	0.972
51DAP/34DAP	1.74341	0.037
52DAP/51DAP	0.95952	1
53DAP/52DAP	1.40489	0.075
55DAP/53DAP	0.77513	0.06
57DAP/55DAP	1.03776	1
62DAP/57DAP	1.16249	0.35
68DAP/62DAP	1.05719	0.885
68DAP/14DAP	1.15011	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02007	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.66888	0.182
Mature Green Tomato/Ripe Tomato	1.10515	0.752
Immature Eggplant/Mature Eggplant	1.35842	0.063
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.3919

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95264	0.944
1-1-2/M82	1.03392	1
12-2/M82	1.06425	1
12-4/M82	1.01799	1
1-3/M82	0.85655	0.501
2-1-1/M82	1.30335	0.689
2-1/M82	1.27304
2-6/M82	1.14464	0.405
3-2/M82	0.85697	0.752
4-1-1/M82	1.13262
4-1/M82	1.106	1
4-3-2/M82	1.01195	0.246
4-3/M82	1.00656
5-3/M82	0.93297	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.04323	1
7-2/M82	1.07848	1
9-3-2/M82	0.9519	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79447
IL2-6/WTpooled	0.94838	1
IL7-5/WTpooled	1.19445	0.792
IL7-3/WTpooled	1.05791	1
IL12-4/WTpooled	1.35689	0.503
IL1-4/WTpooled	1.08647	1
WT/WTpooled	0.98492	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	0.99216	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01021	0.921
DC3000/delta hrp 6h	0.82629	0.942
DC3000/delta hrp 12h	1.01099	1
DC3000/delta hrp 24h	1.07066	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18592	0.068
DC3000 delta B/DC3000 delta AB	1.20149	0.166

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98317	1
Exp 36h	0.86427	0.661
Exp 60h	0.8578	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98683	1
Var 0h	1.02521	1
Var 12h I row2-row1	0.94564	0.856
Var 12h NI row2-row1	1.17618	0.649
Var 36h I row2-row1	1.01694	1
Var 36h NI row2-row1	0.9692	0.791
Var 60h I row2-row1	0.79325	0.374
Var 60h NI row2-row1	0.92184	0.932
Time course 0hI-0hNI	0.92062	0.443
Time course 12hI-12hNI	1.06582	0.593
Time course 36hI-36hNI	1.32144	0.248
Time course 60hI-60hNI	1.56326	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)	0.98433	0.314
transgenic ySAMdc/azygous control (breaker)	0.92996	0.49
transgenic ySAMdc/azygous control (red)	1.07033	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99112	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07434	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.15509	0.09
Manapal/WT (break)	1.47212	0.14
Manapal/WT (red)	1.15126	0.413