Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.6.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09938	0.827
27DAP/17DAP	1.17088	0.809
39DAP/27DAP	1.01087	1
41DAP/39DAP	1.13032	0.696
42DAP/41DAP	1.06046	0.983
43DAP/42DAP	1.06252	1
47DAP/43DAP	1.3293	0.463
52DAP/47DAP	1.19529	0.754
57DAP/52DAP	1.0884	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.98883	0.059
17DAP/reference	2.18232	0.282
27DAP/reference	1.39367	0.339
39DAP/reference	1.23778	0.486
41DAP/reference	0.52186	0.008
42DAP/reference	1.33847	0.182
43DAP/reference	1.12734	0.646
47DAP/reference	0.97814	0.568
52DAP/reference	1.49305	0.011
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04769	0.961
27DAP/17DAP	1.36246	0.079
39DAP/27DAP	0.78127	0.076
41DAP/39DAP	0.93435	0.729
42DAP/41DAP	1.13887	0.571
43DAP/42DAP	0.8856	0.046
47DAP/43DAP	1.02565	0.939
52DAP/47DAP	0.96604	0.893
57DAP/52DAP	1.30882	0.121
57DAP/7DAP	1.48448	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80458	0.115
17DAP/reference	0.77865	0.019
27DAP/reference	0.82267	0.023
39DAP/reference	0.81221	0.083
41DAP/reference	0.80737	0.037
42DAP/reference	0.70769	0.01
43DAP/reference	0.73246	0.011
47DAP/reference	0.89508	0.671
52DAP/reference	0.70998	0.013
57DAP/reference	0.6695	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86088	0.176
17DAP/reference	1.035	0.898
27DAP/reference	1.30733	0.629
39DAP/reference	0.84104	0.067
41DAP/reference	1.24378	0.45
42DAP/reference	1.13744	0.369
43DAP/reference	0.97648	0.633
47DAP/reference	0.91335	0.05
52DAP/reference	1.58249	0.006
57DAP/reference	1.13175	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7942	0.038
17DAP/reference	0.93502	0.56
27DAP/reference	0.96241	0.516
39DAP/reference	0.97739	0.591
41DAP/reference	0.83864	0.07
42DAP/reference	1.34106	0.391
43DAP/reference	1.02684	0.767
47DAP/reference	0.7736	0.357
52DAP/reference	1.26597	0.801
57DAP/reference	1.0939	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.73734
26DAP/20DAP	0.88216	0.512
34DAP/26DAP	0.9747	0.94
51DAP/34DAP	1.12565	0.637
52DAP/51DAP	0.87362	1
53DAP/52DAP	1.012	0.862
55DAP/53DAP	0.83442	0.225
57DAP/55DAP	1.01692	0.925
62DAP/57DAP	1.14046
68DAP/62DAP	0.90347
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80667	0.065

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.3375	0.149
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	3.42645	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07349	0.877
1-1-2/M82	0.84887	0.958
12-2/M82	0.89774	0.955
12-4/M82	0.90171	1
1-3/M82	1.00816	1
2-1-1/M82	1.27222	0.689
2-1/M82	N/A	N/A
2-6/M82	1.11404
3-2/M82	0.74957
4-1-1/M82	0.97951	0.668
4-1/M82	1.1714
4-3-2/M82	0.89109	1
4-3/M82	0.99186	1
5-3/M82	0.87694	1
6-2/M82	1.09495	1
6-3/M82	0.95526	1
7-1/M82	1.1317
7-2/M82	0.77292
9-3-2/M82	0.87506

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27103	0.277
IL2-6/WTpooled	1.13819	0.584
IL7-5/WTpooled	1.55102	0.792
IL7-3/WTpooled	1.03305	1
IL12-4/WTpooled	0.9375	0.539
IL1-4/WTpooled	0.96579	1
WT/WTpooled	0.95012	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	0.769	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02686	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.64827
DC3000/delta hrp 24h	0.82843	0.148

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.42702	0.025
DC3000 delta B/DC3000 delta AB	0.57524	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00894	1
Var 0h	0.93334	1
Var 12h I row2-row1	1.10213	1
Var 12h NI row2-row1	0.88463	0.82
Var 36h I row2-row1	0.94104	1
Var 36h NI row2-row1	1.27774	0.482
Var 60h I row2-row1	1.11728	0.543
Var 60h NI row2-row1	1.00794	1
Time course 0hI-0hNI	0.96868	0.835
Time course 12hI-12hNI	0.8831	0.115
Time course 36hI-36hNI	0.82492	0.036
Time course 60hI-60hNI	0.14857	0.005

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.86638	0.49
transgenic ySAMdc/azygous control (red)	1.07746	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.59698	0.096
Manapal/WT (break)	1.6462	0.183
Manapal/WT (red)	1.10204	1