Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.8.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92122	0.586
27DAP/17DAP	1.38588	0.579
39DAP/27DAP	1.19802	0.635
41DAP/39DAP	1.02809	0.946
42DAP/41DAP	0.94089	1
43DAP/42DAP	0.94788	0.867
47DAP/43DAP	1.06003	0.776
52DAP/47DAP	1.63048	0.193
57DAP/52DAP	1.64678	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95115	0.269
17DAP/reference	0.94581	0.194
27DAP/reference	1.00778	0.996
39DAP/reference	0.93391	0.342
41DAP/reference	1.01749	1
42DAP/reference	0.88287	0.011
43DAP/reference	0.98951	0.805
47DAP/reference	1.04606	0.84
52DAP/reference	0.98639	0.564
57DAP/reference	1.03616	0.447

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85188	0.135
27DAP/17DAP	0.88998	0.724
39DAP/27DAP	1.73984	0.035
41DAP/39DAP	1.77862	0.041
42DAP/41DAP	0.58359	0.017
43DAP/42DAP	1.29393	0.032
47DAP/43DAP	1.01223	0.926
52DAP/47DAP	1.93847	0.061
57DAP/52DAP	2.06469	0.029
57DAP/7DAP	1.32877	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69324	0.043
17DAP/reference	1.29062	0.014
27DAP/reference	1.06522	0.551
39DAP/reference	1.51863	0.007
41DAP/reference	1.05171	0.723
42DAP/reference	1.19902	0.1
43DAP/reference	1.18795	0.124
47DAP/reference	1.0972	0.45
52DAP/reference	1.03612	0.563
57DAP/reference	1.08763	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06382	0.767
17DAP/reference	0.89304	0.297
27DAP/reference	0.88932	0.249
39DAP/reference	1.00044	0.722
41DAP/reference	1.00715	0.749
42DAP/reference	0.95659	0.321
43DAP/reference	1.01085	0.774
47DAP/reference	0.91081	0.051
52DAP/reference	0.95983	0.28
57DAP/reference	0.94629	0.384

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48048	0.033
17DAP/reference	0.93064	0.444
27DAP/reference	1.05006	0.51
39DAP/reference	1.01163	0.858
41DAP/reference	0.97053	0.512
42DAP/reference	1.10142	0.251
43DAP/reference	0.9795	0.59
47DAP/reference	0.93006	0.249
52DAP/reference	1.00178	0.781
57DAP/reference	1.27298	0.129

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26402	0.966
26DAP/20DAP	1.5139	0.112
34DAP/26DAP	1.17385	1
51DAP/34DAP	1.22261	0.137
52DAP/51DAP	0.84376	0.151
53DAP/52DAP	1.73627	0.042
55DAP/53DAP	0.98556	0.852
57DAP/55DAP	0.99008	0.902
62DAP/57DAP	1.07984	0.935
68DAP/62DAP	1.75804	0.012
68DAP/14DAP	1.84815	0.094

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.96172	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.64248	0.176
Mature Green Tomato/Ripe Tomato	0.45165	0.2
Immature Eggplant/Mature Eggplant	0.88763
Ripe Pepper/Ripe Tomato	0.75644	1
Mature Eggplant/Ripe Tomato	0.45263	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.1437
12-2/M82	N/A	N/A
12-4/M82	1.30512
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.59056	0.512
4-3-2/M82	1.8601	0.262
4-3/M82	1.43858	1
5-3/M82	0.87237	0.642
6-2/M82	N/A	N/A
6-3/M82	0.55916
7-1/M82	1.04393
7-2/M82	0.83562
9-3-2/M82	1.44993	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.26517	0.584
IL7-5/WTpooled	0.5583
IL7-3/WTpooled	0.83036	0.418
IL12-4/WTpooled	1.17739	0.785
IL1-4/WTpooled	0.88517	0.834
WT/WTpooled	0.80516	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	1.22435	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94535	1
DC3000/delta hrp 6h	1.09638	0.562
DC3000/delta hrp 12h	0.99815	1
DC3000/delta hrp 24h	1.75756	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.352	0.087
DC3000 delta B/DC3000 delta AB	1.68242	0.118

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16621	1
Exp 36h	0.9821	1
Exp 60h	1.12563	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99919	1
Var 0h	1.25961	0.421
Var 12h I row2-row1	1.14337	0.22
Var 12h NI row2-row1	0.97252	0.906
Var 36h I row2-row1	0.94078	1
Var 36h NI row2-row1	1.17188	1
Var 60h I row2-row1	1.02247	1
Var 60h NI row2-row1	0.99417	1
Time course 0hI-0hNI	1.08961	0.719
Time course 12hI-12hNI	1.57778	0.004
Time course 36hI-36hNI	2.20493	0.004
Time course 60hI-60hNI	2.7996	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)	1.04311	0.511
transgenic ySAMdc/azygous control (breaker)	0.91784	0.251
transgenic ySAMdc/azygous control (red)	0.9276	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98075	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15875	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19893	0.14
Manapal/WT (break)	1.34529	0.14
Manapal/WT (red)	1.31814	0.164