Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29825	0.858
27DAP/17DAP	1.06771	1
39DAP/27DAP	7.26362	0.038
41DAP/39DAP	1.01414	0.919
42DAP/41DAP	1.02186	1
43DAP/42DAP	1.69354	0.867
47DAP/43DAP	0.49176	0.049
52DAP/47DAP	0.74184	0.331
57DAP/52DAP	0.79212	0.588

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57085	0.366
17DAP/reference	0.83518	0.147
27DAP/reference	0.63433	0.036
39DAP/reference	1.508	0.393
41DAP/reference	0.91842	0.267
42DAP/reference	1.98601	0.001
43DAP/reference	2.04697	0.007
47DAP/reference	1.62593	0.001
52DAP/reference	1.03994	1
57DAP/reference	1.02185	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.24613	0.026
27DAP/17DAP	2.13955	0.021
39DAP/27DAP	3.68218	0.034
41DAP/39DAP	2.16285	0.55
42DAP/41DAP	0.97666	0.666
43DAP/42DAP	1.30062	0.086
47DAP/43DAP	1.32975	0.058
52DAP/47DAP	0.52132	0.047
57DAP/52DAP	1.02869	0.848
57DAP/7DAP	1.5651	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.89881	0.024
17DAP/reference	1.04324	0.477
27DAP/reference	1.86855	0.006
39DAP/reference	1.39832	0.013
41DAP/reference	1.7001	0.02
42DAP/reference	3.00999	0.007
43DAP/reference	2.95971	0.007
47DAP/reference	3.97145	0.014
52DAP/reference	3.46119	0.007
57DAP/reference	1.56753	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37911	0.294
17DAP/reference	0.67924	0.086
27DAP/reference	1.82559	0.017
39DAP/reference	1.11107	0.556
41DAP/reference	1.20227	0.157
42DAP/reference	1.46749	0.009
43DAP/reference	1.40767	0.23
47DAP/reference	2.15586	0.02
52DAP/reference	0.57972	0.004
57DAP/reference	1.35293	0.724

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.9316	0.026
17DAP/reference	0.81212	0.186
27DAP/reference	1.33587	0.044
39DAP/reference	2.32794	0.004
41DAP/reference	1.64831	0.006
42DAP/reference	3.14415	0.006
43DAP/reference	3.79761	0.006
47DAP/reference	1.38135	0.093
52DAP/reference	1.62318	0.083
57DAP/reference	0.63054	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98827	1
26DAP/20DAP	1.54616	0.394
34DAP/26DAP	1.06757	1
51DAP/34DAP	0.72313	0.167
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.03253	1
55DAP/53DAP	1.23657	0.566
57DAP/55DAP	1.04869	0.891
62DAP/57DAP	0.87204	0.681
68DAP/62DAP	0.91868	0.668
68DAP/14DAP	1.3196	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	47.2388	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.29072
Mature Green Tomato/Ripe Tomato	0.56876
Immature Eggplant/Mature Eggplant	24.7012	0.05
Ripe Pepper/Ripe Tomato	0.09009	0.224
Mature Eggplant/Ripe Tomato	0.40553	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.38915	0.432
1-1-2/M82	2.41221	1
12-2/M82	0.99241	1
12-4/M82	2.06028	1
1-3/M82	2.4398	0.479
2-1-1/M82	1.15506	0.764
2-1/M82	1.08285	1
2-6/M82	1.69154	0.385
3-2/M82	1.29368	0.967
4-1-1/M82	2.46098	1
4-1/M82	3.18501	0.512
4-3-2/M82	3.22208	0.262
4-3/M82	2.02856	1
5-3/M82	0.89717	1
6-2/M82	2.31041	0.253
6-3/M82	1.15694	1
7-1/M82	0.99671	1
7-2/M82	1.17948	1
9-3-2/M82	3.64304	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.1908	0.584
IL7-5/WTpooled	0.85172
IL7-3/WTpooled	0.81768	0.418
IL12-4/WTpooled	0.87016	0.71
IL1-4/WTpooled	0.99726	0.834
WT/WTpooled	1.00504	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	1.53765	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03981	0.921
DC3000/delta hrp 6h	1.38626	1
DC3000/delta hrp 12h	0.97109	1
DC3000/delta hrp 24h	3.21025	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.46728	0.042
DC3000 delta B/DC3000 delta AB	3.96241	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.47855	0.228
Exp 36h	2.5847	0.349
Exp 60h	2.80708	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.65052	0.26
transgenic ySAMdc/azygous control (breaker)	1.26059	0.178
transgenic ySAMdc/azygous control (red)	1.36423	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02613	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.55233	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74326	1
Manapal/WT (break)	1.14398	0.183
Manapal/WT (red)	1.05879	1