Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.11.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23378	1
27DAP/17DAP	1.45659	0.688
39DAP/27DAP	1.51264	0.229
41DAP/39DAP	0.72917	0.113
42DAP/41DAP	1.02863	1
43DAP/42DAP	0.98523	0.909
47DAP/43DAP	0.89431	0.645
52DAP/47DAP	1.70382	0.211
57DAP/52DAP	1.19334	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95388	0.442
17DAP/reference	0.75922	0.025
27DAP/reference	0.89932	0.339
39DAP/reference	0.79538	0.149
41DAP/reference	0.8198	0.201
42DAP/reference	1.6763	0.001
43DAP/reference	1.17999	0.126
47DAP/reference	1.16008	0.085
52DAP/reference	0.7127	0.041
57DAP/reference	0.94965	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85498	0.158
27DAP/17DAP	0.87555	0.614
39DAP/27DAP	1.38515	0.054
41DAP/39DAP	1.64433	0.163
42DAP/41DAP	0.64837	0.015
43DAP/42DAP	1.09446	0.351
47DAP/43DAP	1.11484	0.65
52DAP/47DAP	1.5092	0.172
57DAP/52DAP	1.6914	0.029
57DAP/7DAP	1.28617	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05022	0.843
17DAP/reference	1.01824	1
27DAP/reference	1.58152	0.009
39DAP/reference	1.28789	0.186
41DAP/reference	1.53402	0.011
42DAP/reference	2.47058	0.006
43DAP/reference	2.29529	0.007
47DAP/reference	1.90371	0.014
52DAP/reference	1.73933	0.011
57DAP/reference	2.47157	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.55458	0.007
17DAP/reference	0.89742	0.149
27DAP/reference	1.14067	0.192
39DAP/reference	0.77049	0.034
41DAP/reference	1.1867	0.052
42DAP/reference	1.35729	0.013
43DAP/reference	1.04499	0.569
47DAP/reference	1.95618	0.01
52DAP/reference	0.57109	0.003
57DAP/reference	1.10252	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8155	0.063
17DAP/reference	0.76759	0.15
27DAP/reference	1.24157	0.059
39DAP/reference	1.16981	0.218
41DAP/reference	0.84854	0.019
42DAP/reference	1.03892	0.994
43DAP/reference	1.04696	0.923
47DAP/reference	1.17505	0.68
52DAP/reference	1.37506	0.038
57DAP/reference	1.53244	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89167	1
26DAP/20DAP	1.42021	0.24
34DAP/26DAP	0.89357	0.412
51DAP/34DAP	1.72114	0.032
52DAP/51DAP	0.82991	0.151
53DAP/52DAP	1.45217	0.04
55DAP/53DAP	0.72554	0.14
57DAP/55DAP	0.97236	0.789
62DAP/57DAP	0.64676	0.088
68DAP/62DAP	1.63617	0.405
68DAP/14DAP	1.05651	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.57737	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	0.38285	0.021
Immature Eggplant/Mature Eggplant	8.4927	0.05
Ripe Pepper/Ripe Tomato	0.12846	0.224
Mature Eggplant/Ripe Tomato	0.08075	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87847	0.934
1-1-2/M82	0.87909	0.958
12-2/M82	1.37868	0.61
12-4/M82	1.12207	0.611
1-3/M82	3.52485	0.248
2-1-1/M82	1.58295	0.375
2-1/M82	1.317
2-6/M82	1.92921	0.425
3-2/M82	1.35129	0.84
4-1-1/M82	2.90954	0.977
4-1/M82	2.17798
4-3-2/M82	2.16556	0.241
4-3/M82	1.80259	0.268
5-3/M82	0.86149	1
6-2/M82	4.02247	0.253
6-3/M82	1.93089	1
7-1/M82	0.97755	1
7-2/M82	2.48042	0.318
9-3-2/M82	1.45589	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93426
IL2-6/WTpooled	0.73308	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.22961	0.362
IL12-4/WTpooled	1.11528	0.785
IL1-4/WTpooled	0.83562
WT/WTpooled	1.03213	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	1.40927	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04521	0.921
DC3000/delta hrp 6h	1.2241	1
DC3000/delta hrp 12h	1.08177	1
DC3000/delta hrp 24h	1.8082	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32802	0.102
DC3000 delta B/DC3000 delta AB	1.40432	0.096

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.51088	1
Exp 36h	2.63751	0.489
Exp 60h	1.80141	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99237	1
Var 0h	1.42778	0.98
Var 12h I row2-row1	1.12417	0.324
Var 12h NI row2-row1	1.01584	1
Var 36h I row2-row1	1.10849	1
Var 36h NI row2-row1	0.8266	0.378
Var 60h I row2-row1	1.00174	1
Var 60h NI row2-row1	0.82297	0.431
Time course 0hI-0hNI	1.01324	0.833
Time course 12hI-12hNI	1.89922	0.004
Time course 36hI-36hNI	2.86437	0.004
Time course 60hI-60hNI	3.43096	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)	1.05815	1
transgenic ySAMdc/azygous control (breaker)	0.66469	0.142
transgenic ySAMdc/azygous control (red)	1.08289	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.70171	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7844	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.80461	1
Manapal/WT (break)	0.79478	1
Manapal/WT (red)	0.96867	0.728