Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.12.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96823	0.77
27DAP/17DAP	0.87372	0.72
39DAP/27DAP	0.89354	0.537
41DAP/39DAP	0.97939	0.839
42DAP/41DAP	0.9814	1
43DAP/42DAP	1.16064	1
47DAP/43DAP	1.09556	0.979
52DAP/47DAP	0.7798	0.461
57DAP/52DAP	0.85546	0.8

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23625	0.062
17DAP/reference	1.19001	0.048
27DAP/reference	1.22832	0.054
39DAP/reference	1.49033	0.054
41DAP/reference	1.82085	0.016
42DAP/reference	1.22368	0.01
43DAP/reference	1.07013	0.758
47DAP/reference	1.25377	0.19
52DAP/reference	1.29901	0.088
57DAP/reference	1.27313	0.6

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27148	0.076
27DAP/17DAP	0.83305	0.614
39DAP/27DAP	0.84183	0.222
41DAP/39DAP	1.02386	0.909
42DAP/41DAP	0.97842	0.776
43DAP/42DAP	0.85714	0.089
47DAP/43DAP	0.98827	0.896
52DAP/47DAP	1.13184	0.666
57DAP/52DAP	1.09818	0.703
57DAP/7DAP	0.71075	0.143

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78526	0.146
17DAP/reference	0.93195	0.22
27DAP/reference	1.44877	0.008
39DAP/reference	0.76646	0.039
41DAP/reference	0.8268	0.079
42DAP/reference	0.98945	0.612
43DAP/reference	0.78946	0.027
47DAP/reference	0.89068	0.383
52DAP/reference	0.69762	0.012
57DAP/reference	0.68129	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24657	0.915
17DAP/reference	2.17831	0.007
27DAP/reference	2.02717	0.013
39DAP/reference	1.68958	0.04
41DAP/reference	2.02298	0.005
42DAP/reference	1.82003	0.009
43DAP/reference	1.91337	0.016
47DAP/reference	1.90932	0.009
52DAP/reference	2.22964	0.008
57DAP/reference	1.80392	0.075

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90364	0.23
17DAP/reference	1.16658	0.824
27DAP/reference	0.93503	0.23
39DAP/reference	0.90692	0.076
41DAP/reference	1.15426	0.197
42DAP/reference	1.45283	0.013
43DAP/reference	1.19607	0.973
47DAP/reference	1.25682	0.147
52DAP/reference	1.10703	0.542
57DAP/reference	1.52886	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07372	1
26DAP/20DAP	1.08836	0.988
34DAP/26DAP	1.198	1
51DAP/34DAP	0.67127	0.071
52DAP/51DAP	0.80339	0.151
53DAP/52DAP	0.7025	0.101
55DAP/53DAP	0.84281	0.462
57DAP/55DAP	1.25544	0.881
62DAP/57DAP	1.04066	1
68DAP/62DAP	1.21397	0.971
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.36267	0.035

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.34229	0.04
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	1.04338

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05709	1
1-1-2/M82	0.94514
12-2/M82	N/A	N/A
12-4/M82	1.13171	1
1-3/M82	1.14682
2-1-1/M82	1.08812
2-1/M82	N/A	N/A
2-6/M82	0.84448	1
3-2/M82	0.839
4-1-1/M82	0.99533	1
4-1/M82	0.9647
4-3-2/M82	1.11813	0.284
4-3/M82	0.76128	0.72
5-3/M82	0.97661	1
6-2/M82	N/A	N/A
6-3/M82	0.97351
7-1/M82	N/A	N/A
7-2/M82	0.68431
9-3-2/M82	0.86198	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04889	0.493
IL2-6/WTpooled	1.00869	1
IL7-5/WTpooled	1.25816	0.792
IL7-3/WTpooled	1.20404	1
IL12-4/WTpooled	1.10134	0.695
IL1-4/WTpooled	1.23523	0.426
WT/WTpooled	0.91591	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	0.84049	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05525	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.2155	1
DC3000/delta hrp 24h	0.93727	0.43

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.48498
DC3000 delta B/DC3000 delta AB	0.66204	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05948	1
Exp 36h	N/A	N/A
Exp 60h	1.05722	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02935	1
Var 0h	1.13101	0.98
Var 12h I row2-row1	0.82385	0.353
Var 12h NI row2-row1	0.89769	0.713
Var 36h I row2-row1	0.71369	1
Var 36h NI row2-row1	1.19625	1
Var 60h I row2-row1	1.30401	0.562
Var 60h NI row2-row1	1.09385	0.904
Time course 0hI-0hNI	0.98733	0.999
Time course 12hI-12hNI	0.95076	0.436
Time course 36hI-36hNI	0.854	0.023
Time course 60hI-60hNI	0.30521	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)	1.21577	0.612
transgenic ySAMdc/azygous control (breaker)	1.26136	0.248
transgenic ySAMdc/azygous control (red)	1.05048	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89646	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2309	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.00641	1
Manapal/WT (red)	1.11814	1