Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08632	0.561
27DAP/17DAP	1.02736	0.905
39DAP/27DAP	0.884	0.495
41DAP/39DAP	1.27189	0.179
42DAP/41DAP	1.0492	1
43DAP/42DAP	1.05098	1
47DAP/43DAP	1.06082	0.405
52DAP/47DAP	0.92074	0.758
57DAP/52DAP	1.05283	0.958

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94425	0.344
17DAP/reference	0.98257	0.63
27DAP/reference	0.97363	0.552
39DAP/reference	1.00415	0.8
41DAP/reference	0.97583	0.667
42DAP/reference	0.98656	0.425
43DAP/reference	0.94946	0.538
47DAP/reference	0.96386	0.035
52DAP/reference	0.94484	0.183
57DAP/reference	0.9896	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99926	0.899
27DAP/17DAP	1.02386	0.942
39DAP/27DAP	0.98469	0.833
41DAP/39DAP	1.03822	0.807
42DAP/41DAP	0.97492	0.762
43DAP/42DAP	1.04763	0.297
47DAP/43DAP	0.9748	0.757
52DAP/47DAP	0.99265	0.947
57DAP/52DAP	0.97424	0.584
57DAP/7DAP	0.94691	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95744	0.445
17DAP/reference	1.20311	0.054
27DAP/reference	1.12541	0.246
39DAP/reference	1.07468	0.634
41DAP/reference	1.1303	0.402
42DAP/reference	1.32904	0.021
43DAP/reference	1.06279	0.923
47DAP/reference	0.8554	0.128
52DAP/reference	1.19941	0.459
57DAP/reference	0.91691	0.149

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03082	0.885
17DAP/reference	1.06094	0.083
27DAP/reference	0.93294	0.203
39DAP/reference	0.95478	0.497
41DAP/reference	1.1564	0.573
42DAP/reference	0.95545	0.189
43DAP/reference	1.18916	0.373
47DAP/reference	0.97037	0.107
52DAP/reference	N/A	N/A
57DAP/reference	1.00445	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95014	0.092
17DAP/reference	1.0561	0.854
27DAP/reference	1.02573	0.624
39DAP/reference	1.03871	0.512
41DAP/reference	1.05979	0.777
42DAP/reference	1.05364	0.961
43DAP/reference	0.93913	0.432
47DAP/reference	0.99699	0.731
52DAP/reference	0.95726	0.582
57DAP/reference	0.8826	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00848	0.966
26DAP/20DAP	1.0254	0.988
34DAP/26DAP	1.0365	1
51DAP/34DAP	0.98141	0.799
52DAP/51DAP	0.9932	1
53DAP/52DAP	1.03291	0.921
55DAP/53DAP	0.90065	0.43
57DAP/55DAP	1.16628	0.764
62DAP/57DAP	0.80863	0.466
68DAP/62DAP	0.972	0.834
68DAP/14DAP	1.03881	0.785

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.77988	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.03316	0.898
Immature Eggplant/Mature Eggplant	0.85018	0.067
Ripe Pepper/Ripe Tomato	1.46525
Mature Eggplant/Ripe Tomato	1.66839

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09172	0.877
1-1-2/M82	0.93534	1
12-2/M82	0.98016	0.955
12-4/M82	1.00213	1
1-3/M82	0.9117	0.501
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.97475	1
3-2/M82	0.93479	1
4-1-1/M82	0.96425	1
4-1/M82	0.97721	1
4-3-2/M82	0.98417	1
4-3/M82	1.04099	1
5-3/M82	0.96794	1
6-2/M82	1.08723	0.253
6-3/M82	1.02447
7-1/M82	0.89706	0.803
7-2/M82	0.99224	1
9-3-2/M82	0.88624	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.81759	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.02858	0.293
IL12-4/WTpooled	1.13711	0.516
IL1-4/WTpooled	0.84367
WT/WTpooled	1.00999	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	0.9457	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99893	1
DC3000/delta hrp 6h	1.12463	1
DC3000/delta hrp 12h	0.96733	1
DC3000/delta hrp 24h	1.00563	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17584	0.229
DC3000 delta B/DC3000 delta AB	1.01914	0.687

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96292	1
Exp 36h	0.82134	0.374
Exp 60h	0.67536	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.90059	0.457
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.94715	0.454
transgenic ySAMdc/azygous control (breaker)	1.63461	0.248
transgenic ySAMdc/azygous control (red)	1.26205	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98784	0.444

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.78306	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.41789	0.105
Manapal/WT (break)	1.83702	0.183
Manapal/WT (red)	2.7796	0.126