Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.12.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52609	0.219
27DAP/17DAP	1.01266	0.984
39DAP/27DAP	0.98636	0.782
41DAP/39DAP	1.04959	0.92
42DAP/41DAP	1.4825	0.722
43DAP/42DAP	0.84992	0.705
47DAP/43DAP	0.88015	0.562
52DAP/47DAP	1.05284	0.997
57DAP/52DAP	0.85016	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93671	0.362
17DAP/reference	1.27298	0.039
27DAP/reference	1.31532	0.032
39DAP/reference	1.40257	0.157
41DAP/reference	1.42957	0.014
42DAP/reference	1.65148	0.001
43DAP/reference	1.08885	0.73
47DAP/reference	0.90057	0.224
52DAP/reference	0.94101	0.36
57DAP/reference	0.9603	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96794	0.697
27DAP/17DAP	0.97323	0.887
39DAP/27DAP	1.18054	0.292
41DAP/39DAP	0.85673	0.228
42DAP/41DAP	1.16388	0.273
43DAP/42DAP	1.05963	0.478
47DAP/43DAP	0.9511	0.75
52DAP/47DAP	1.02066	0.956
57DAP/52DAP	1.20947	0.115
57DAP/7DAP	0.94433	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02494	1
17DAP/reference	1.0629	0.328
27DAP/reference	1.13557	0.041
39DAP/reference	1.4859	0.053
41DAP/reference	1.157	0.232
42DAP/reference	0.96538	0.458
43DAP/reference	1.04918	0.637
47DAP/reference	0.82209	0.168
52DAP/reference	0.86077	0.072
57DAP/reference	0.92075	0.144

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82716	0.145
17DAP/reference	1.587	0.026
27DAP/reference	1.24484	0.526
39DAP/reference	1.46188	0.041
41DAP/reference	1.228	0.382
42DAP/reference	1.20778	0.195
43DAP/reference	1.21053	0.255
47DAP/reference	1.50831	0.016
52DAP/reference	0.90805	0.239
57DAP/reference	1.11044	0.593

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03911	0.793
17DAP/reference	0.98263	0.601
27DAP/reference	1.15615	0.085
39DAP/reference	0.94201	0.122
41DAP/reference	1.14968	0.108
42DAP/reference	1.40535	0.111
43DAP/reference	1.23608	1
47DAP/reference	0.90388	0.199
52DAP/reference	0.98051	0.732
57DAP/reference	1.3158	0.16

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97436	1
26DAP/20DAP	0.97155	1
34DAP/26DAP	1.16636	1
51DAP/34DAP	1.00265	0.967
52DAP/51DAP	1.31277	0.034
53DAP/52DAP	0.90532	0.544
55DAP/53DAP	1.03595	0.964
57DAP/55DAP	0.92546	0.619
62DAP/57DAP	0.95447	0.871
68DAP/62DAP	1.05307	0.914
68DAP/14DAP	0.63311	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87952	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.90611	0.522
Immature Eggplant/Mature Eggplant	0.95493	0.72
Ripe Pepper/Ripe Tomato	0.23096
Mature Eggplant/Ripe Tomato	8.55568	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.45177
1-1-2/M82	1.75948	1
12-2/M82	0.70406
12-4/M82	0.85015	1
1-3/M82	0.73643	0.501
2-1-1/M82	1.94764	0.457
2-1/M82	N/A	N/A
2-6/M82	0.83039	1
3-2/M82	0.62261
4-1-1/M82	N/A	N/A
4-1/M82	2.16024
4-3-2/M82	1.31623	1
4-3/M82	0.82129	1
5-3/M82	0.99158	1
6-2/M82	1.36159	1
6-3/M82	1.51095	1
7-1/M82	0.91845	1
7-2/M82	1.03272	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82126
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01242
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	3.92565	1
WT/WTpooled	0.84283	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	1.20522	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09629	0.846
DC3000/delta hrp 6h	1.2361	0.672
DC3000/delta hrp 12h	1.91437	1
DC3000/delta hrp 24h	0.84619	0.285

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97393	0.92
DC3000 delta B/DC3000 delta AB	0.89267	0.326

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.1779	1
Exp 36h	0.82576	0.623
Exp 60h	0.7074	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00645	1
Var 0h	1.04595	0.98
Var 12h I row2-row1	0.87184	0.418
Var 12h NI row2-row1	1.07114	1
Var 36h I row2-row1	1.14051	0.368
Var 36h NI row2-row1	1.20553	0.482
Var 60h I row2-row1	0.82634	0.374
Var 60h NI row2-row1	0.95107	1
Time course 0hI-0hNI	1.01217	1
Time course 12hI-12hNI	0.97991	0.886
Time course 36hI-36hNI	0.89546	0.15
Time course 60hI-60hNI	0.59505	0.006

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)	0.69174	0.32
transgenic ySAMdc/azygous control (breaker)	0.84713	0.49
transgenic ySAMdc/azygous control (red)	0.76739	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95429	0.153

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.10627	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.42008	1
Manapal/WT (break)	0.86024	1
Manapal/WT (red)	1.11325	0.15