Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.5.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93146	0.683
27DAP/17DAP	0.87719	0.713
39DAP/27DAP	1.1792	1
41DAP/39DAP	0.84599	0.412
42DAP/41DAP	0.80949	1
43DAP/42DAP	0.79048	0.527
47DAP/43DAP	0.70686	0.185
52DAP/47DAP	0.92883	0.688
57DAP/52DAP	1.1831	0.962

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28522	0.049
17DAP/reference	1.18187	0.154
27DAP/reference	1.26947	0.032
39DAP/reference	1.27592	0.025
41DAP/reference	1.22692	0.036
42DAP/reference	1.1772	0.065
43DAP/reference	1.08259	0.812
47DAP/reference	0.93687	0.098
52DAP/reference	0.95486	0.427
57DAP/reference	1.12843	0.379

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87906
27DAP/17DAP	0.99612	1
39DAP/27DAP	0.89139
41DAP/39DAP	0.73362
42DAP/41DAP	1.03122	1
43DAP/42DAP	1.22499
47DAP/43DAP	1.42481
52DAP/47DAP	1.08862
57DAP/52DAP	1.24079
57DAP/7DAP	0.84543

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1299	0.231
17DAP/reference	1.04779	0.688
27DAP/reference	1.09994	0.301
39DAP/reference	0.95481	0.307
41DAP/reference	1.01518	1
42DAP/reference	1.13441	0.059
43DAP/reference	1.07123	0.148
47DAP/reference	1.16324	0.149
52DAP/reference	1.0881	0.171
57DAP/reference	1.11978	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42534	0.038
17DAP/reference	1.45163	0.009
27DAP/reference	1.30394	0.039
39DAP/reference	1.3657	0.017
41DAP/reference	1.4021	0.027
42DAP/reference	1.4747	0.008
43DAP/reference	1.38323	0.085
47DAP/reference	1.40316	0.008
52DAP/reference	1.05756	0.938
57DAP/reference	1.28725	0.127

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11311	0.237
17DAP/reference	1.16254	0.162
27DAP/reference	1.00939	1
39DAP/reference	1.14441	0.12
41DAP/reference	0.96171	0.293
42DAP/reference	1.07967	0.265
43DAP/reference	1.00554	0.767
47DAP/reference	1.04709	0.847
52DAP/reference	1.26766	0.284
57DAP/reference	1.05707	0.786

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	4.62464	0.966
26DAP/20DAP	N/A	N/A
34DAP/26DAP	1.92228	0.819
51DAP/34DAP	N/A	N/A
52DAP/51DAP	N/A	N/A
53DAP/52DAP	4.78561
55DAP/53DAP	1.41229
57DAP/55DAP	1.21388
62DAP/57DAP	N/A	N/A
68DAP/62DAP	0.81604	0.787
68DAP/14DAP	2.07961

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.65501	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.06142	0.666
Mature Green Tomato/Ripe Tomato	1.38675	0.948
Immature Eggplant/Mature Eggplant	0.7813	0.062
Ripe Pepper/Ripe Tomato	0.45968	0.224
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	0.97562	1
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.06384
7-2/M82	N/A	N/A
9-3-2/M82	1.2154

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	1.11403	1
IL12-4/WTpooled	0.87586	1
IL1-4/WTpooled	2.61856	0.426
WT/WTpooled	1.21703	0.957

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.95322	0.95
DC3000/delta hrp 12h	1.04194	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16306	1
Exp 36h	1.30289	0.489
Exp 60h	1.53834	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.90415	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	1.2194
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.01572	0.921
transgenic ySAMdc/azygous control (breaker)	0.8061	0.251
transgenic ySAMdc/azygous control (red)	1.14978	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10728	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.56314	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90451	1
Manapal/WT (break)	0.9788	1
Manapal/WT (red)	0.93387	0.181