Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.9.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.49372	0.264
27DAP/17DAP	1.36353	0.656
39DAP/27DAP	2.29192	0.2
41DAP/39DAP	1.35999	0.676
42DAP/41DAP	1.19139	0.941
43DAP/42DAP	1.15013	1
47DAP/43DAP	0.43504	0.049
52DAP/47DAP	0.85201	0.609
57DAP/52DAP	0.86772	0.745

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61914	0.031
17DAP/reference	0.78726	0.009
27DAP/reference	0.99854	0.822
39DAP/reference	0.80774	0.047
41DAP/reference	0.84559	0.201
42DAP/reference	1.7915	0.001
43DAP/reference	0.78659	0.118
47DAP/reference	0.75882	0.004
52DAP/reference	0.77597	0.102
57DAP/reference	1.05983	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89916	0.454
27DAP/17DAP	0.83135	0.418
39DAP/27DAP	1.83777	0.1
41DAP/39DAP	3.10324	0.005
42DAP/41DAP	0.59794	0.008
43DAP/42DAP	0.50861	0.022
47DAP/43DAP	1.05518	0.827
52DAP/47DAP	1.3868	0.681
57DAP/52DAP	0.54584	0.137
57DAP/7DAP	0.84492	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66693	0.059
17DAP/reference	2.28473	0.269
27DAP/reference	2.0347	0.107
39DAP/reference	2.33311	0.141
41DAP/reference	0.82701	0.111
42DAP/reference	1.72658	0.405
43DAP/reference	1.15391	1
47DAP/reference	2.14544	0.037
52DAP/reference	2.17579	0.013
57DAP/reference	2.94261	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6848	0.029
17DAP/reference	0.85295	0.164
27DAP/reference	0.82122	0.049
39DAP/reference	2.3376	0.025
41DAP/reference	1.38033	0.014
42DAP/reference	1.5951	0.202
43DAP/reference	2.61244	0.052
47DAP/reference	3.82861	0.01
52DAP/reference	1.26714	0.106
57DAP/reference	4.42987	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08473	0.489
17DAP/reference	1.25472	0.746
27DAP/reference	0.80334	0.03
39DAP/reference	1.4196	0.075
41DAP/reference	1.6554	0.056
42DAP/reference	0.77912	0.108
43DAP/reference	0.69089	0.043
47DAP/reference	0.65793	0.006
52DAP/reference	0.74705	0.123
57DAP/reference	0.96192	0.475

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.44104	0.966
26DAP/20DAP	1.02486	1
34DAP/26DAP	0.99883	0.945
51DAP/34DAP	0.76748	0.193
52DAP/51DAP	0.78948	1
53DAP/52DAP	1.17212	0.868
55DAP/53DAP	0.82457	0.303
57DAP/55DAP	1.32229	0.643
62DAP/57DAP	0.96806	0.994
68DAP/62DAP	0.93947	0.787
68DAP/14DAP	0.56823	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.79233	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	3.48435	0.015
Immature Eggplant/Mature Eggplant	169.453	0.165
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.29056

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94203	0.961
1-1-2/M82	1.76334
12-2/M82	2.99601
12-4/M82	1.52949	1
1-3/M82	2.20654	0.479
2-1-1/M82	N/A	N/A
2-1/M82	4.27021	0.312
2-6/M82	1.57753
3-2/M82	4.11987	0.463
4-1-1/M82	3.61747
4-1/M82	1.27834
4-3-2/M82	N/A	N/A
4-3/M82	1.00757
5-3/M82	1.82674	0.378
6-2/M82	12.2778
6-3/M82	0.34805	0.916
7-1/M82	0.14525	0.466
7-2/M82	2.61523	0.318
9-3-2/M82	2.51459	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14755	0.277
IL2-6/WTpooled	1.31726	0.531
IL7-5/WTpooled	1.2738	0.792
IL7-3/WTpooled	1.53466	1
IL12-4/WTpooled	1.06989	0.646
IL1-4/WTpooled	0.99899	1
WT/WTpooled	0.96958	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	1.51401	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97011	1
DC3000/delta hrp 6h	1.11371	1
DC3000/delta hrp 12h	1.25936	1
DC3000/delta hrp 24h	2.30523	0.03

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.52928	0.042
DC3000 delta B/DC3000 delta AB	2.56877	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.67205	1
Exp 36h	1.61032	0.693
Exp 60h	2.92469	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97175	1
Var 0h	0.83977	0.933
Var 12h I row2-row1	0.75686	0.514
Var 12h NI row2-row1	1.77798	0.34
Var 36h I row2-row1	1.28082	1
Var 36h NI row2-row1	0.60276	0.549
Var 60h I row2-row1	0.81329	0.582
Var 60h NI row2-row1	0.72172	0.572
Time course 0hI-0hNI	1.27343	0.63
Time course 12hI-12hNI	1.23859	0.684
Time course 36hI-36hNI	3.31751	0.011
Time course 60hI-60hNI	7.63852	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)	0.37155	0.229
transgenic ySAMdc/azygous control (breaker)	0.44324	0.137
transgenic ySAMdc/azygous control (red)	1.10866	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99323	0.784

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.13653	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18609	1
Manapal/WT (break)	0.38869	0.333
Manapal/WT (red)	0.23163	0.242