Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.11.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.78918	0.272
27DAP/17DAP	0.75596	0.366
39DAP/27DAP	0.97662	0.67
41DAP/39DAP	0.83714	0.392
42DAP/41DAP	0.55604	0.397
43DAP/42DAP	0.95718	0.909
47DAP/43DAP	1.29364	0.513
52DAP/47DAP	1.29889	0.895
57DAP/52DAP	1.004	0.982

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24647	0.101
17DAP/reference	1.33284	0.021
27DAP/reference	1.46694	0.018
39DAP/reference	1.14051	0.119
41DAP/reference	1.24219	0.043
42DAP/reference	1.03501	0.756
43DAP/reference	0.9565	0.48
47DAP/reference	0.8793	0.046
52DAP/reference	0.86574	0.118
57DAP/reference	0.7409	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00883	0.847
27DAP/17DAP	1.26875	0.407
39DAP/27DAP	0.45147	0.033
41DAP/39DAP	0.94097	0.885
42DAP/41DAP	0.91431	0.425
43DAP/42DAP	0.7069	0.034
47DAP/43DAP	0.66949	0.056
52DAP/47DAP	1.60766	0.1
57DAP/52DAP	1.34704	0.282
57DAP/7DAP	0.58012	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.58979	0.039
17DAP/reference	1.62516	0.077
27DAP/reference	1.20862	0.131
39DAP/reference	1.346	0.059
41DAP/reference	1.12101	0.241
42DAP/reference	1.26671	0.405
43DAP/reference	1.00817	0.727
47DAP/reference	1.14871	0.421
52DAP/reference	0.86166	0.046
57DAP/reference	1.39038	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26331	0.051
17DAP/reference	1.49144	0.007
27DAP/reference	2.40918	0.102
39DAP/reference	1.10857	0.463
41DAP/reference	1.07362	0.831
42DAP/reference	1.05667	0.649
43DAP/reference	0.90246	0.277
47DAP/reference	0.89737	0.042
52DAP/reference	1.13228	0.106
57DAP/reference	0.96263	0.488

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06879	0.659
17DAP/reference	1.31072	0.111
27DAP/reference	1.29786	0.028
39DAP/reference	1.39265	0.13
41DAP/reference	1.32074	0.056
42DAP/reference	0.94268	0.552
43DAP/reference	0.96061	0.568
47DAP/reference	0.89052	0.168
52DAP/reference	1.36337	0.428
57DAP/reference	0.93222	0.326

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0584	0.966
26DAP/20DAP	0.87011	1
34DAP/26DAP	1.003	0.988
51DAP/34DAP	0.78101	0.197
52DAP/51DAP	1.62656	0.033
53DAP/52DAP	0.69875	0.065
55DAP/53DAP	1.82197	0.042
57DAP/55DAP	0.73326	0.14
62DAP/57DAP	1.23176	0.303
68DAP/62DAP	1.02225	0.885
68DAP/14DAP	0.73932	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.40386	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.43356	0.058
Mature Green Tomato/Ripe Tomato	18.2678
Immature Eggplant/Mature Eggplant	0.21473	0.064
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	58.259	0.268

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	N/A	N/A
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	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.7909	0.243
IL2-6/WTpooled	1.29785	0.456
IL7-5/WTpooled	1.31844	1
IL7-3/WTpooled	1.04269	1
IL12-4/WTpooled	0.75898	0.71
IL1-4/WTpooled	1.33177	0.417
WT/WTpooled	0.88862	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	0.67721	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11359	0.692
DC3000/delta hrp 6h	0.862	0.95
DC3000/delta hrp 12h	1.11961	1
DC3000/delta hrp 24h	0.63167	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8595	0.099
DC3000 delta B/DC3000 delta AB	1.01678	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86426	1
Exp 36h	0.94191	0.82
Exp 60h	0.95274	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00749	1
Var 0h	0.44505	0.933
Var 12h I row2-row1	0.86331	0.353
Var 12h NI row2-row1	0.89091	0.546
Var 36h I row2-row1	1.09497	1
Var 36h NI row2-row1	0.94425	1
Var 60h I row2-row1	0.99186	1
Var 60h NI row2-row1	1.196	0.904
Time course 0hI-0hNI	0.94218	0.522
Time course 12hI-12hNI	0.74732	0.033
Time course 36hI-36hNI	0.77175	0.052
Time course 60hI-60hNI	0.27804	0.005

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)	1.17454	0.321
transgenic ySAMdc/azygous control (breaker)	0.99062	1
transgenic ySAMdc/azygous control (red)	1.09051	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93148	0.056

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.60498	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28113	1
Manapal/WT (break)	1.16716	0.381
Manapal/WT (red)	N/A	N/A