Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.8.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.06781	0.033
27DAP/17DAP	1.13529	0.847
39DAP/27DAP	1.97737	0.105
41DAP/39DAP	0.65017	0.064
42DAP/41DAP	1.18948	0.873
43DAP/42DAP	1.05998	1
47DAP/43DAP	0.88322	0.613
52DAP/47DAP	0.84057	0.581
57DAP/52DAP	1.4581	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93546	0.379
17DAP/reference	1.41371	0.026
27DAP/reference	1.79922	0.008
39DAP/reference	1.45547	0.075
41DAP/reference	1.57721	0.03
42DAP/reference	1.91299	0.001
43DAP/reference	1.75776	0.007
47DAP/reference	2.45586	0.001
52DAP/reference	2.47936	0.007
57DAP/reference	1.93348	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.4562	0.036
27DAP/17DAP	1.19668	0.458
39DAP/27DAP	0.94385	0.721
41DAP/39DAP	1.3729	1
42DAP/41DAP	1.38386	0.425
43DAP/42DAP	0.88605	0.351
47DAP/43DAP	0.96274	0.861
52DAP/47DAP	1.09383	0.835
57DAP/52DAP	1.26925	0.197
57DAP/7DAP	1.97558	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25119	0.311
17DAP/reference	1.37507	0.016
27DAP/reference	2.07927	0.008
39DAP/reference	2.873	0.005
41DAP/reference	2.39848	0.008
42DAP/reference	2.52926	0.007
43DAP/reference	2.75665	0.006
47DAP/reference	3.40009	0.014
52DAP/reference	2.86051	0.007
57DAP/reference	3.21638	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63675	0.012
17DAP/reference	1.12588	0.385
27DAP/reference	1.8654	0.014
39DAP/reference	2.28578	0.011
41DAP/reference	1.87782	0.005
42DAP/reference	2.11915	0.007
43DAP/reference	1.25742	0.827
47DAP/reference	2.11038	0.008
52DAP/reference	1.64766	0.006
57DAP/reference	1.06443	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77783	0.033
17DAP/reference	0.8396	0.089
27DAP/reference	1.64193	0.014
39DAP/reference	1.93813	0.005
41DAP/reference	1.69457	0.007
42DAP/reference	2.39014	0.006
43DAP/reference	2.28538	0.006
47DAP/reference	2.19662	0.006
52DAP/reference	2.14549	0.028
57DAP/reference	2.87692	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28136	0.586
26DAP/20DAP	1.45181	0.153
34DAP/26DAP	1.1145	0.542
51DAP/34DAP	0.81283	0.24
52DAP/51DAP	0.73625	0.151
53DAP/52DAP	1.10025	0.398
55DAP/53DAP	0.72723	0.017
57DAP/55DAP	1.55481	0.324
62DAP/57DAP	1.32106	0.01
68DAP/62DAP	1.42499	0.076
68DAP/14DAP	0.93212	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.66191	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79815	0.274
Mature Green Tomato/Ripe Tomato	1.35314	0.814
Immature Eggplant/Mature Eggplant	1.45946	0.05
Ripe Pepper/Ripe Tomato	0.78443	0.293
Mature Eggplant/Ripe Tomato	0.76726	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97272	0.961
1-1-2/M82	1.38037	1
12-2/M82	1.12222	1
12-4/M82	1.45874	1
1-3/M82	2.52403	0.248
2-1-1/M82	1.02266	1
2-1/M82	0.68457	0.519
2-6/M82	0.77318	1
3-2/M82	1.25105	0.967
4-1-1/M82	1.31664	0.977
4-1/M82	1.89196	0.853
4-3-2/M82	1.16448	0.508
4-3/M82	1.03487	0.268
5-3/M82	0.94454	1
6-2/M82	1.34427	1
6-3/M82	0.99006	1
7-1/M82	1.14581	1
7-2/M82	1.27448	1
9-3-2/M82	1.2566	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.12848
IL1-4/WTpooled	1.21203
WT/WTpooled	N/A	N/A

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	1.07483	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13038	0.692
DC3000/delta hrp 6h	1.00169	0.95
DC3000/delta hrp 12h	1.1021	1
DC3000/delta hrp 24h	0.92585	0.306

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01638	1
DC3000 delta B/DC3000 delta AB	1.05339	0.528

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08088	1
Exp 36h	1.12655	1
Exp 60h	1.11588	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0037	1
Var 0h	0.77744	0.933
Var 12h I row2-row1	1.06414	0.654
Var 12h NI row2-row1	0.96442	0.906
Var 36h I row2-row1	1.12975	0.601
Var 36h NI row2-row1	1.39771	0.482
Var 60h I row2-row1	0.77741	0.439
Var 60h NI row2-row1	0.9902	1
Time course 0hI-0hNI	1.04551	0.833
Time course 12hI-12hNI	0.99326	1
Time course 36hI-36hNI	1.03588	0.722
Time course 60hI-60hNI	1.32353	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)	1.14326	0.654
transgenic ySAMdc/azygous control (breaker)	1.09979	0.248
transgenic ySAMdc/azygous control (red)	1.22409	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.53355	0.08

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0133	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92227	1
Manapal/WT (break)	0.99761	1
Manapal/WT (red)	0.99517	1