Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86051	0.364
27DAP/17DAP	1.15505	0.845
39DAP/27DAP	1.48999	0.287
41DAP/39DAP	0.93418	0.678
42DAP/41DAP	0.79354	0.774
43DAP/42DAP	1.10864	1
47DAP/43DAP	0.84029	0.504
52DAP/47DAP	1.23081	0.769
57DAP/52DAP	1.40292	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79954	0.085
17DAP/reference	1.04604	1
27DAP/reference	1.00972	0.923
39DAP/reference	1.13012	0.453
41DAP/reference	0.97188	0.667
42DAP/reference	7.52364	0.001
43DAP/reference	4.56583	0.009
47DAP/reference	3.69899	0.004
52DAP/reference	1.15334	0.371
57DAP/reference	1.00468	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13789	0.29
27DAP/17DAP	1.01714	1
39DAP/27DAP	1.04276	0.751
41DAP/39DAP	1.07209	1
42DAP/41DAP	1.00536	0.869
43DAP/42DAP	0.90528	0.308
47DAP/43DAP	1.04591	0.914
52DAP/47DAP	1.08431	0.862
57DAP/52DAP	1.18385	0.444
57DAP/7DAP	1.11229	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89511	0.168
17DAP/reference	1.03088	1
27DAP/reference	0.95542	0.303
39DAP/reference	0.93476	0.354
41DAP/reference	1.01172	0.848
42DAP/reference	1.16441	0.1
43DAP/reference	1.09334	1
47DAP/reference	1.15473	0.514
52DAP/reference	0.79837	0.097
57DAP/reference	0.84512	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92163	0.426
17DAP/reference	0.90105	0.297
27DAP/reference	0.89091	0.188
39DAP/reference	0.81623	0.189
41DAP/reference	0.92409	0.103
42DAP/reference	1.16155	0.476
43DAP/reference	1.00923	0.774
47DAP/reference	0.89129	0.232
52DAP/reference	0.90269	0.203
57DAP/reference	0.85746	0.298

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93303	0.422
17DAP/reference	0.84893	0.286
27DAP/reference	1.13369	0.078
39DAP/reference	0.99969	0.693
41DAP/reference	1.09158	0.621
42DAP/reference	1.42703	0.214
43DAP/reference	4.29335	0.07
47DAP/reference	3.58636	0.006
52DAP/reference	2.31645	0.123
57DAP/reference	1.14309	0.462

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97411	1
26DAP/20DAP	1.46454	0.128
34DAP/26DAP	0.84061	0.301
51DAP/34DAP	1.27236	0.121
52DAP/51DAP	0.95532	1
53DAP/52DAP	1.35448	0.097
55DAP/53DAP	0.66046	0.032
57DAP/55DAP	0.8916	0.499
62DAP/57DAP	0.80045	0.162
68DAP/62DAP	3.11887	0.316
68DAP/14DAP	1.05944	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.60959	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02756	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.28495	0.293
Mature Eggplant/Ripe Tomato	1.04152	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96112	1
12-2/M82	N/A	N/A
12-4/M82	1.10678	1
1-3/M82	N/A	N/A
2-1-1/M82	1.33806
2-1/M82	N/A	N/A
2-6/M82	1.05426	0.695
3-2/M82	0.98492
4-1-1/M82	N/A	N/A
4-1/M82	1.225	1
4-3-2/M82	1.38589
4-3/M82	0.69153	0.611
5-3/M82	0.93286	1
6-2/M82	N/A	N/A
6-3/M82	1.02198	1
7-1/M82	N/A	N/A
7-2/M82	0.8544
9-3-2/M82	1.1741	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.34519
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.11744	0.395
WT/WTpooled	N/A	N/A

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	1.06717	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.13807	0.921
DC3000/delta hrp 6h	0.87058
DC3000/delta hrp 12h	0.89277	1
DC3000/delta hrp 24h	0.93116	0.607

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26316	0.076
DC3000 delta B/DC3000 delta AB	1.38439	0.09

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99777	1
Var 0h	0.91725	1
Var 12h I row2-row1	0.96503	0.948
Var 12h NI row2-row1	1.11818	1
Var 36h I row2-row1	1.18257	0.489
Var 36h NI row2-row1	1.04822	1
Var 60h I row2-row1	0.81459	0.439
Var 60h NI row2-row1	0.94369	1
Time course 0hI-0hNI	0.93877	0.629
Time course 12hI-12hNI	1.10211	0.403
Time course 36hI-36hNI	1.38633	0.008
Time course 60hI-60hNI	1.86208	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)	1.19166	0.511
transgenic ySAMdc/azygous control (breaker)	7.21929	0.166
transgenic ySAMdc/azygous control (red)	1.5272	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9457	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.71982	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87558	1
Manapal/WT (break)	1.46622	1
Manapal/WT (red)	0.69066	0.199