Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13725	0.878
27DAP/17DAP	0.98211	0.959
39DAP/27DAP	1.45478	0.159
41DAP/39DAP	0.76945	0.247
42DAP/41DAP	1.11584	0.994
43DAP/42DAP	1.00259	0.937
47DAP/43DAP	1.04241	0.953
52DAP/47DAP	0.89693	0.683
57DAP/52DAP	0.99054	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94821	0.362
17DAP/reference	1.039	0.318
27DAP/reference	1.04081	0.559
39DAP/reference	1.02488	0.664
41DAP/reference	1.05512	0.287
42DAP/reference	0.92434	0.091
43DAP/reference	1.08092	0.34
47DAP/reference	1.14214	0.114
52DAP/reference	0.95937	0.416
57DAP/reference	0.88868	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44085	0.036
27DAP/17DAP	1.1902	0.279
39DAP/27DAP	1.10754	0.453
41DAP/39DAP	1.01429	1
42DAP/41DAP	1.16026	0.225
43DAP/42DAP	0.83602	0.127
47DAP/43DAP	1.15875	0.325
52DAP/47DAP	0.96753	0.893
57DAP/52DAP	0.62237	0.066
57DAP/7DAP	0.75593	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52241	0.039
17DAP/reference	0.902	0.064
27DAP/reference	0.91525	0.117
39DAP/reference	0.96134	0.354
41DAP/reference	0.96104	0.394
42DAP/reference	1.01677	0.791
43DAP/reference	0.85208	0.082
47DAP/reference	1.15365	0.345
52DAP/reference	0.98652	0.571
57DAP/reference	1.00189	0.775

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96096	0.607
17DAP/reference	0.78311	0.008
27DAP/reference	0.75315	0.01
39DAP/reference	0.65929	0.016
41DAP/reference	0.72904	0.044
42DAP/reference	0.81065	0.028
43DAP/reference	0.95586	0.478
47DAP/reference	0.97706	0.487
52DAP/reference	0.76836	0.004
57DAP/reference	1.0212	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15909	0.045
17DAP/reference	0.86696	0.198
27DAP/reference	0.8385	0.038
39DAP/reference	1.00771	0.889
41DAP/reference	0.88186	0.05
42DAP/reference	0.94312	0.287
43DAP/reference	0.9101	0.294
47DAP/reference	1.05289	0.294
52DAP/reference	0.88397	0.247
57DAP/reference	0.75139	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04492	0.966
26DAP/20DAP	2.06893	0.21
34DAP/26DAP	0.94904	0.857
51DAP/34DAP	3.26627	0.032
52DAP/51DAP	1.09388	0.676
53DAP/52DAP	0.82788	0.167
55DAP/53DAP	0.52729	0.016
57DAP/55DAP	1.1676	0.265
62DAP/57DAP	1.06186	0.935
68DAP/62DAP	1.59711	0.472
68DAP/14DAP	2.11543	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47853	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6737	0.179
Mature Green Tomato/Ripe Tomato	0.83914	0.03
Immature Eggplant/Mature Eggplant	1.50883	0.067
Ripe Pepper/Ripe Tomato	1.85382	0.256
Mature Eggplant/Ripe Tomato	0.8663	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0612	0.574
1-1-2/M82	1.06089	1
12-2/M82	1.03494	1
12-4/M82	1.29403	1
1-3/M82	0.9878	1
2-1-1/M82	1.07826	0.764
2-1/M82	0.87009	0.74
2-6/M82	1.31829	0.452
3-2/M82	0.57408	0.455
4-1-1/M82	1.1041	1
4-1/M82	1.45893	1
4-3-2/M82	1.56914	0.262
4-3/M82	2.58196	0.268
5-3/M82	1.11151	1
6-2/M82	1.21238	0.235
6-3/M82	0.95981	1
7-1/M82	0.92216	0.803
7-2/M82	0.75663	0.881
9-3-2/M82	1.664	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.98156	1
IL2-6/WTpooled	0.90467	1
IL7-5/WTpooled	0.78693	1
IL7-3/WTpooled	1.04375	1
IL12-4/WTpooled	1.04615	0.785
IL1-4/WTpooled	0.87815	0.699
WT/WTpooled	1.0946	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	0.93527	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9666	1
DC3000/delta hrp 6h	1.1141	1
DC3000/delta hrp 12h	0.88153	1
DC3000/delta hrp 24h	1.50392	0.048

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.64717	0.042
DC3000 delta B/DC3000 delta AB	1.51196	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.39066	1
Exp 36h	1.29523	0.693
Exp 60h	1.07149	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9668	1
Var 0h	1.28553	0.936
Var 12h I row2-row1	1.15922	0.272
Var 12h NI row2-row1	1.03181	0.649
Var 36h I row2-row1	1.02415	1
Var 36h NI row2-row1	1.04809	1
Var 60h I row2-row1	0.86367	0.832
Var 60h NI row2-row1	0.9056	0.818
Time course 0hI-0hNI	1.04994	0.852
Time course 12hI-12hNI	1.15723	0.062
Time course 36hI-36hNI	1.35055	0.128
Time course 60hI-60hNI	1.60305	0.022

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)	1.03073	0.482
transgenic ySAMdc/azygous control (breaker)	0.59105	0.134
transgenic ySAMdc/azygous control (red)	0.93417	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94217	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09064	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0056	1
Manapal/WT (break)	0.80954	0.299
Manapal/WT (red)	0.95383	0.728