Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.17.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05394	0.919
27DAP/17DAP	1.05187	0.911
39DAP/27DAP	0.67735	0.286
41DAP/39DAP	1.06389	0.54
42DAP/41DAP	0.96202	1
43DAP/42DAP	0.944	0.877
47DAP/43DAP	1.15808	0.769
52DAP/47DAP	1.11556	0.902
57DAP/52DAP	1.36696	0.883

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87252	0.172
17DAP/reference	0.68425	0.007
27DAP/reference	0.83088	0.013
39DAP/reference	0.80038	0.009
41DAP/reference	0.62103	0.008
42DAP/reference	0.97224	0.337
43DAP/reference	0.78331	0.017
47DAP/reference	0.99185	0.473
52DAP/reference	1.47306	0.079
57DAP/reference	1.44651	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07453	0.687
27DAP/17DAP	1.0466	0.9
39DAP/27DAP	1.19589	0.168
41DAP/39DAP	1.02061	0.914
42DAP/41DAP	1.22859	0.241
43DAP/42DAP	0.99947	1
47DAP/43DAP	1.00255	1
52DAP/47DAP	0.99289	0.947
57DAP/52DAP	1.01222	1
57DAP/7DAP	0.99111	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13996	0.311
17DAP/reference	1.09753	0.269
27DAP/reference	0.93438	0.094
39DAP/reference	1.14523	0.028
41DAP/reference	1.17608	0.27
42DAP/reference	1.10375	0.308
43DAP/reference	0.94791	0.368
47DAP/reference	0.97708	0.671
52DAP/reference	0.85895	0.012
57DAP/reference	0.78744	0.036

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83299	0.17
17DAP/reference	0.7504	0.012
27DAP/reference	0.97518	0.519
39DAP/reference	1.14483	0.449
41DAP/reference	1.175	0.199
42DAP/reference	1.02505	0.899
43DAP/reference	0.68163	0.014
47DAP/reference	0.84176	0.045
52DAP/reference	1.01963	1
57DAP/reference	0.62354	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93874	0.29
17DAP/reference	0.8977	0.281
27DAP/reference	1.0059	0.805
39DAP/reference	0.88705	0.012
41DAP/reference	0.99487	0.754
42DAP/reference	1.09338	0.961
43DAP/reference	1.15001	0.895
47DAP/reference	0.95165	0.409
52DAP/reference	1.02406	0.871
57DAP/reference	2.03938	0.014

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.86567	0.997
26DAP/20DAP	1.67023	0.33
34DAP/26DAP	1.29807	0.819
51DAP/34DAP	1.76623	0.032
52DAP/51DAP	0.82507	1
53DAP/52DAP	1.63776	0.028
55DAP/53DAP	0.86667	0.033
57DAP/55DAP	1.0435	0.875
62DAP/57DAP	0.95642	0.871
68DAP/62DAP	2.36543	0.066
68DAP/14DAP	3.6282	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78973	0.102

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.94414
Mature Green Tomato/Ripe Tomato	1.02075	0.835
Immature Eggplant/Mature Eggplant	1.6801	0.078
Ripe Pepper/Ripe Tomato	0.70482	0.293
Mature Eggplant/Ripe Tomato	0.84117	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20996	0.591
1-1-2/M82	1.13869	1
12-2/M82	1.24598
12-4/M82	0.92317	0.619
1-3/M82	0.97065
2-1-1/M82	0.5778
2-1/M82	1.42821
2-6/M82	0.83216	0.501
3-2/M82	1.15757	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.99466	1
5-3/M82	1.01058	1
6-2/M82	0.77459
6-3/M82	0.96203	1
7-1/M82	0.88201	0.803
7-2/M82	0.8149
9-3-2/M82	0.89113	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.87182	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.71427	0.294
IL12-4/WTpooled	1.23856	0.624
IL1-4/WTpooled	0.95138	0.699
WT/WTpooled	0.85972	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	0.81688	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96538	1
DC3000/delta hrp 6h	1.05694	1
DC3000/delta hrp 12h	0.9427	1
DC3000/delta hrp 24h	1.23665	0.136

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.63698
DC3000 delta B/DC3000 delta AB	1.46459	0.304

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.67748	1
Exp 36h	1.03629	1
Exp 60h	1.26159	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02352	1
Var 0h	1.01055	1
Var 12h I row2-row1	1.2093	0.263
Var 12h NI row2-row1	1.14233	0.649
Var 36h I row2-row1	1.03406	1
Var 36h NI row2-row1	1.03122	1
Var 60h I row2-row1	0.84664	0.285
Var 60h NI row2-row1	1.37571	0.904
Time course 0hI-0hNI	0.95106	0.623
Time course 12hI-12hNI	1.04371	0.693
Time course 36hI-36hNI	1.04618	0.128
Time course 60hI-60hNI	1.23482	0.047

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)	0.989	0.789
transgenic ySAMdc/azygous control (breaker)	1.45751	0.178
transgenic ySAMdc/azygous control (red)	1.06008	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87796	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88737	1
Manapal/WT (break)	0.94613	1
Manapal/WT (red)	0.64517	0.181