Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04666	1
27DAP/17DAP	0.61212	0.082
39DAP/27DAP	0.81895	0.39
41DAP/39DAP	0.60359	0.053
42DAP/41DAP	1.16319	1
43DAP/42DAP	1.14435	0.861
47DAP/43DAP	0.56343	0.069
52DAP/47DAP	0.83396	0.559
57DAP/52DAP	1.30956	0.946

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0493	0.96
17DAP/reference	0.96351	0.567
27DAP/reference	1.14986	0.096
39DAP/reference	1.03621	0.903
41DAP/reference	1.1573	0.158
42DAP/reference	1.28933	0.001
43DAP/reference	0.98948	0.745
47DAP/reference	1.32255	0.006
52DAP/reference	1.03655	1
57DAP/reference	1.12945	0.332

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84542	0.036
27DAP/17DAP	0.77794	0.295
39DAP/27DAP	0.56514	0.029
41DAP/39DAP	1.29575	0.497
42DAP/41DAP	0.90245	0.377
43DAP/42DAP	0.77454	0.026
47DAP/43DAP	1.00672	0.973
52DAP/47DAP	0.8131	0.203
57DAP/52DAP	1.35364	0.543
57DAP/7DAP	0.46148	0.149

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91871	0.27
17DAP/reference	0.93173	0.108
27DAP/reference	1.10963	0.088
39DAP/reference	0.89444	0.034
41DAP/reference	0.80389	0.01
42DAP/reference	0.80577	0.014
43DAP/reference	0.8269	0.026
47DAP/reference	1.05642	0.854
52DAP/reference	0.81468	0.031
57DAP/reference	0.82484	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92974	0.457
17DAP/reference	1.35675	0.014
27DAP/reference	1.37107	0.08
39DAP/reference	1.42432	0.051
41DAP/reference	1.47657	0.019
42DAP/reference	1.46424	0.009
43DAP/reference	1.13087	0.462
47DAP/reference	1.15778	0.069
52DAP/reference	1.13324	0.106
57DAP/reference	0.9327	0.338

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96131	0.214
17DAP/reference	1.11445	0.474
27DAP/reference	0.96756	0.465
39DAP/reference	1.0311	0.987
41DAP/reference	1.03749	0.439
42DAP/reference	1.17983	0.3
43DAP/reference	1.25118	0.432
47DAP/reference	1.36803	0.104
52DAP/reference	0.95728	0.611
57DAP/reference	1.48637	0.074

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.75094	0.966
26DAP/20DAP	1.0928	0.974
34DAP/26DAP	0.88853	0.479
51DAP/34DAP	0.43509	0.049
52DAP/51DAP	1.07111	0.77
53DAP/52DAP	0.63499	0.073
55DAP/53DAP	0.99673	0.886
57DAP/55DAP	0.93416	0.817
62DAP/57DAP	1.26775	0.8
68DAP/62DAP	0.8624	0.406
68DAP/14DAP	0.51403	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74408	0.129

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.60348	0.058
Mature Green Tomato/Ripe Tomato	4.34879	0.015
Immature Eggplant/Mature Eggplant	0.7191	0.117
Ripe Pepper/Ripe Tomato	0.93366	1
Mature Eggplant/Ripe Tomato	2.00063

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	1.2458
1-3/M82	N/A	N/A
2-1-1/M82	1.55535
2-1/M82	N/A	N/A
2-6/M82	1.40646
3-2/M82	1.17037
4-1-1/M82	0.9319
4-1/M82	N/A	N/A
4-3-2/M82	1.74601
4-3/M82	N/A	N/A
5-3/M82	0.86949
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.96677
7-2/M82	N/A	N/A
9-3-2/M82	1.11575	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.16395	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02704	1
IL12-4/WTpooled	1.03827	0.839
IL1-4/WTpooled	1.26827	1
WT/WTpooled	1.04739	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	1.28679	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96341	1
DC3000/delta hrp 6h	1.101	1
DC3000/delta hrp 12h	1.24496	1
DC3000/delta hrp 24h	1.06748	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56163	0.029
DC3000 delta B/DC3000 delta AB	0.41361	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98302	1
Exp 36h	0.82618	0.699
Exp 60h	0.6807	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98337	1
Var 0h	0.98104	1
Var 12h I row2-row1	0.86072	0.39
Var 12h NI row2-row1	0.99546	1
Var 36h I row2-row1	0.90408	0.805
Var 36h NI row2-row1	0.92055	0.706
Var 60h I row2-row1	1.52054	0.562
Var 60h NI row2-row1	1.04506	1
Time course 0hI-0hNI	1.01448	1
Time course 12hI-12hNI	0.99092	0.984
Time course 36hI-36hNI	1.01706	0.799
Time course 60hI-60hNI	0.30844	0.009

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)	0.96738	0.614
transgenic ySAMdc/azygous control (breaker)	1.15796	1
transgenic ySAMdc/azygous control (red)	1.0353	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.71429	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.92665	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.0422	0.087
Manapal/WT (break)	1.24481	1
Manapal/WT (red)	1.21224	0.413