Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.3.19.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1314	0.977
27DAP/17DAP	1.65911	0.346
39DAP/27DAP	1.57597	0.504
41DAP/39DAP	0.7736	0.238
42DAP/41DAP	0.96734	1
43DAP/42DAP	0.98989	0.918
47DAP/43DAP	1.31288	0.633
52DAP/47DAP	1.2673	0.745
57DAP/52DAP	1.37909	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24912	0.179
17DAP/reference	1.27452	0.04
27DAP/reference	1.06626	0.885
39DAP/reference	1.34747	0.028
41DAP/reference	1.69914	0.015
42DAP/reference	1.25766	0.001
43DAP/reference	1.02195	0.787
47DAP/reference	1.07517	0.433
52DAP/reference	1.19413	0.083
57DAP/reference	0.8992	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.65486	0.129
27DAP/17DAP	1.09971	0.621
39DAP/27DAP	1.22464	0.331
41DAP/39DAP	1.13131	0.674
42DAP/41DAP	0.88598	0.279
43DAP/42DAP	0.89813	0.308
47DAP/43DAP	1.14437	0.359
52DAP/47DAP	1.05817	0.835
57DAP/52DAP	1.27995	0.089
57DAP/7DAP	1.33459	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80852	0.122
17DAP/reference	0.71728	0.011
27DAP/reference	0.6431	0.01
39DAP/reference	0.83225	0.018
41DAP/reference	0.75895	0.018
42DAP/reference	0.76743	0.011
43DAP/reference	0.74725	0.013
47DAP/reference	0.72369	0.128
52DAP/reference	0.70701	0.011
57DAP/reference	0.77073	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86744	0.069
17DAP/reference	1.35154	0.052
27DAP/reference	1.30087	0.278
39DAP/reference	1.07619	0.477
41DAP/reference	1.3933	0.146
42DAP/reference	1.17279	0.259
43DAP/reference	1.65051	0.313
47DAP/reference	1.28673	0.009
52DAP/reference	1.2227	0.667
57DAP/reference	1.35845	0.306

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97438	0.607
17DAP/reference	1.01192	0.87
27DAP/reference	0.711	0.042
39DAP/reference	0.80644	0.058
41DAP/reference	1.0739	0.867
42DAP/reference	0.94099	0.445
43DAP/reference	1.00363	0.827
47DAP/reference	1.12839	0.877
52DAP/reference	0.99292	0.704
57DAP/reference	0.97158	0.613

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9621	1
26DAP/20DAP	1.28102	0.409
34DAP/26DAP	1.38367	0.304
51DAP/34DAP	1.63084	0.062
52DAP/51DAP	1.1459	0.596
53DAP/52DAP	1.06996	1
55DAP/53DAP	0.98737	0.908
57DAP/55DAP	1.17074	0.71
62DAP/57DAP	0.96405	0.994
68DAP/62DAP	2.45536	0.95
68DAP/14DAP	0.94662	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.31707	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.66777	0.042
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.63167	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.60467	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.83178	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.97175	N/A
7-2/M82	0.66701	N/A
9-3-2/M82	0.52244	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.48099	N/A
IL2-6/WTpooled	0.52523	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.89001	0.362
IL12-4/WTpooled	1.28656	0.891
IL1-4/WTpooled	1.29848	0.395
WT/WTpooled	1.00474	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	1.1152	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05896	0.846
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.09745	1
DC3000/delta hrp 24h	0.97552	0.861

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26311	0.208
DC3000 delta B/DC3000 delta AB	1.86566	0.169

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9913	N/A
Var 0h	1.19922	0.374
Var 12h I row2-row1	0.85893	0.338
Var 12h NI row2-row1	0.98729	0.906
Var 36h I row2-row1	1.02093	1
Var 36h NI row2-row1	1.04647	0.276
Var 60h I row2-row1	0.9112	0.832
Var 60h NI row2-row1	0.81999	0.318
Time course 0hI-0hNI	1.09361	0.344
Time course 12hI-12hNI	0.99426	1
Time course 36hI-36hNI	1.11564	0.355
Time course 60hI-60hNI	1.85224	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.88213	0.173
transgenic ySAMdc/azygous control (red)	0.8795	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93595	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.74446	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00394	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.72748	0.164