Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.6.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4915	0.073
27DAP/17DAP	0.99036	1
39DAP/27DAP	0.99703	0.782
41DAP/39DAP	0.83654	0.362
42DAP/41DAP	0.91331	1
43DAP/42DAP	0.99286	0.937
47DAP/43DAP	0.99002	0.934
52DAP/47DAP	1.34662	0.297
57DAP/52DAP	1.07475	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96114	0.412
17DAP/reference	0.97271	0.63
27DAP/reference	1.00716	1
39DAP/reference	0.99611	0.941
41DAP/reference	0.95945	0.341
42DAP/reference	0.94615	0.124
43DAP/reference	1.08418	0.382
47DAP/reference	0.87837	0.019
52DAP/reference	0.84595	0.019
57DAP/reference	0.91542	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.7322	0.036
27DAP/17DAP	0.96655	0.878
39DAP/27DAP	1.19389	0.369
41DAP/39DAP	0.99681	1
42DAP/41DAP	1.00798	0.887
43DAP/42DAP	0.6993	0.022
47DAP/43DAP	0.98787	0.947
52DAP/47DAP	1.18177	0.586
57DAP/52DAP	1.30167	0.066
57DAP/7DAP	2.05089	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03077	1
17DAP/reference	1.3732	0.07
27DAP/reference	1.29583	0.017
39DAP/reference	1.73092	0.077
41DAP/reference	1.22288	0.223
42DAP/reference	1.36328	0.046
43DAP/reference	1.1843	0.14
47DAP/reference	1.26786	0.241
52DAP/reference	1.44045	0.011
57DAP/reference	1.4456	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97093	0.639
17DAP/reference	0.90717	0.106
27DAP/reference	0.89608	0.129
39DAP/reference	0.86705	0.093
41DAP/reference	0.81285	0.031
42DAP/reference	0.83001	0.02
43DAP/reference	0.92564	0.32
47DAP/reference	0.84647	0.014
52DAP/reference	0.90314	0.086
57DAP/reference	0.99917	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14969	0.366
17DAP/reference	0.954	0.601
27DAP/reference	1.09016	0.575
39DAP/reference	1.11111	0.218
41DAP/reference	1.2151	0.174
42DAP/reference	1.21271	0.34
43DAP/reference	1.00045	0.66
47DAP/reference	0.94273	0.383
52DAP/reference	1.07529	0.601
57DAP/reference	0.73261	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16082	0.966
26DAP/20DAP	2.07684	0.153
34DAP/26DAP	1.14794	1
51DAP/34DAP	1.26489	0.377
52DAP/51DAP	0.67068	0.151
53DAP/52DAP	1.19402	0.444
55DAP/53DAP	0.96779	0.784
57DAP/55DAP	1.10258	0.927
62DAP/57DAP	0.95019	0.994
68DAP/62DAP	1.16039	0.872
68DAP/14DAP	1.11485	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.97473	0.015

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.63013
Mature Green Tomato/Ripe Tomato	0.76741	0.024
Immature Eggplant/Mature Eggplant	1.42572
Ripe Pepper/Ripe Tomato	0.21214
Mature Eggplant/Ripe Tomato	1.11159	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3454	0.536
1-1-2/M82	1.09431	1
12-2/M82	1.15831	1
12-4/M82	0.96261	0.298
1-3/M82	N/A	N/A
2-1-1/M82	0.98919	1
2-1/M82	1.25955
2-6/M82	0.83957	1
3-2/M82	0.85917	0.752
4-1-1/M82	N/A	N/A
4-1/M82	1.13313
4-3-2/M82	0.82265	0.698
4-3/M82	0.86398	1
5-3/M82	0.93619	1
6-2/M82	0.77208
6-3/M82	1.04689	1
7-1/M82	0.84874
7-2/M82	1.05327	1
9-3-2/M82	0.80289	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.20468	0.493
IL2-6/WTpooled	0.92816	1
IL7-5/WTpooled	0.91064	1
IL7-3/WTpooled	1.14571	1
IL12-4/WTpooled	0.81693	0.554
IL1-4/WTpooled	0.96159	0.834
WT/WTpooled	0.89875	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	0.89066	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99218	1
DC3000/delta hrp 6h	0.9	0.95
DC3000/delta hrp 12h	1.06378	1
DC3000/delta hrp 24h	1.08431	0.567

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	2.30997	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99696	1
Exp 36h	1.6932	0.489
Exp 60h	1.46592	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03474	1
Var 0h	1.26934	0.421
Var 12h I row2-row1	1.23239	0.348
Var 12h NI row2-row1	0.97609	0.906
Var 36h I row2-row1	0.91295	1
Var 36h NI row2-row1	1.3879	1
Var 60h I row2-row1	0.93966	0.582
Var 60h NI row2-row1	0.91127	0.932
Time course 0hI-0hNI	0.97324	0.886
Time course 12hI-12hNI	1.06494	0.668
Time course 36hI-36hNI	0.96653	0.46
Time course 60hI-60hNI	0.93512	0.319

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)	1.01403	0.312
transgenic ySAMdc/azygous control (breaker)	1.49324	0.172
transgenic ySAMdc/azygous control (red)	1.08564	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02549	0.177

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.63605	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1161	0.307
Manapal/WT (break)	0.84294	1
Manapal/WT (red)	1.07621	1