Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.3.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11015	0.904
27DAP/17DAP	1.22656	0.804
39DAP/27DAP	0.98196	0.663
41DAP/39DAP	1.38633	0.451
42DAP/41DAP	1.03286	1
43DAP/42DAP	1.02634	0.937
47DAP/43DAP	1.00385	0.89
52DAP/47DAP	1.00062	0.897
57DAP/52DAP	0.98925	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95088	0.379
17DAP/reference	1.13823	0.055
27DAP/reference	1.12907	0.314
39DAP/reference	0.98432	0.855
41DAP/reference	0.88997	0.542
42DAP/reference	1.31926	0.544
43DAP/reference	1.15985
47DAP/reference	0.94842	0.161
52DAP/reference	0.93566	0.449
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96968	0.663
27DAP/17DAP	1.03751	0.9
39DAP/27DAP	0.94564	0.265
41DAP/39DAP	1.03006	0.88
42DAP/41DAP	0.99251	0.865
43DAP/42DAP	1.03811	0.122
47DAP/43DAP	0.99182	0.977
52DAP/47DAP	0.97771	0.902
57DAP/52DAP	0.92844	0.445
57DAP/7DAP	0.99447	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06954	0.555
17DAP/reference	0.60471	0.094
27DAP/reference	0.57313	0.016
39DAP/reference	0.79806	0.126
41DAP/reference	0.95101	0.431
42DAP/reference	0.66056	0.013
43DAP/reference	0.99132	0.459
47DAP/reference	0.93129	0.504
52DAP/reference	0.75708	0.083
57DAP/reference	1.04774	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15659	0.261
17DAP/reference	1.03937	0.806
27DAP/reference	0.86772	0.123
39DAP/reference	0.77041	0.136
41DAP/reference	0.8621	0.145
42DAP/reference	0.94567	0.321
43DAP/reference	0.94748	0.378
47DAP/reference	1.0011	1
52DAP/reference	0.6204	0.156
57DAP/reference	0.88254	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85564	0.335
17DAP/reference	0.84616	0.537
27DAP/reference	0.68952	0.319
39DAP/reference	0.83351	0.393
41DAP/reference	0.89355	0.331
42DAP/reference	0.55999	0.014
43DAP/reference	0.8102	0.281
47DAP/reference	0.9485	0.315
52DAP/reference	0.76881	0.296
57DAP/reference	0.76057	0.048

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07962	0.878
26DAP/20DAP	0.96005	1
34DAP/26DAP	1.00612	1
51DAP/34DAP	0.9717	0.747
52DAP/51DAP	1.04208	0.662
53DAP/52DAP	1.06416	0.783
55DAP/53DAP	1.02525	1
57DAP/55DAP	1.07309	0.955
62DAP/57DAP	0.94254	0.871
68DAP/62DAP	0.87217	0.747
68DAP/14DAP	0.63755	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87008	0.052

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01635	0.726
Mature Green Tomato/Ripe Tomato	0.8542	0.347
Immature Eggplant/Mature Eggplant	1.39947	0.085
Ripe Pepper/Ripe Tomato	1.03977
Mature Eggplant/Ripe Tomato	1.43413	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98826	0.961
1-1-2/M82	0.98967	1
12-2/M82	0.91554	0.862
12-4/M82	0.9749	1
1-3/M82	0.95715	1
2-1-1/M82	1.11614	0.422
2-1/M82	N/A	N/A
2-6/M82	1.16413	0.425
3-2/M82	1.10566
4-1-1/M82	0.8649	0.985
4-1/M82	0.99953	1
4-3-2/M82	0.91562	1
4-3/M82	1.12996
5-3/M82	0.93932	0.642
6-2/M82	0.90838	1
6-3/M82	0.97819	1
7-1/M82	1.04901	1
7-2/M82	1.05779	1
9-3-2/M82	0.70826	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91406	1
IL2-6/WTpooled	0.84253	0.473
IL7-5/WTpooled	0.94062	1
IL7-3/WTpooled	0.79987	1
IL12-4/WTpooled	0.8969	1
IL1-4/WTpooled	0.72951	0.476
WT/WTpooled	1.01679	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	0.73979	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02246	1
DC3000/delta hrp 6h	0.93516	0.95
DC3000/delta hrp 12h	1.16433	1
DC3000/delta hrp 24h	1.06302	0.62

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15555	0.044
DC3000 delta B/DC3000 delta AB	1.0516	0.51

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97151	1
Exp 36h	1.12622	1
Exp 60h	0.87378	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	0.89666
Var 0h	0.85487	0.933
Var 12h I row2-row1	0.94505	0.627
Var 12h NI row2-row1	1.11931	0.649
Var 36h I row2-row1	1.42313	0.908
Var 36h NI row2-row1	1.77852	1
Var 60h I row2-row1	0.8729	0.285
Var 60h NI row2-row1	1.14851	0.904
Time course 0hI-0hNI	0.92548	0.522
Time course 12hI-12hNI	0.9457	0.606
Time course 36hI-36hNI	0.90472	0.136
Time course 60hI-60hNI	0.34502	0.005

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)	1.04433	0.397
transgenic ySAMdc/azygous control (breaker)	0.71786	0.142
transgenic ySAMdc/azygous control (red)	0.94449	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96931	0.064

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.26042	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73876	0.172
Manapal/WT (break)	1.12757	1
Manapal/WT (red)	1.16785	0.413