Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.8.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89188	0.522
27DAP/17DAP	1.00735	0.973
39DAP/27DAP	2.04057	0.095
41DAP/39DAP	1.51523	0.359
42DAP/41DAP	1.8763	0.024
43DAP/42DAP	1.36575	0.296
47DAP/43DAP	1.30291	0.442
52DAP/47DAP	0.71377	0.211
57DAP/52DAP	0.84954	0.74

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91822	0.159
17DAP/reference	1.1104	0.04
27DAP/reference	1.03964	0.66
39DAP/reference	1.08333	0.343
41DAP/reference	1.02447	0.808
42DAP/reference	0.81744	0.006
43DAP/reference	1.04297	0.36
47DAP/reference	0.88211	0.032
52DAP/reference	0.92416	0.25
57DAP/reference	0.90973	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7233	0.078
27DAP/17DAP	1.20873	0.37
39DAP/27DAP	2.33902	0.044
41DAP/39DAP	0.429	0.013
42DAP/41DAP	2.50698	0.003
43DAP/42DAP	6.69111	0.013
47DAP/43DAP	1.16914	0.798
52DAP/47DAP	0.79923	0.46
57DAP/52DAP	0.74814	0.141
57DAP/7DAP	4.53466	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62808	0.06
17DAP/reference	0.74231	0.072
27DAP/reference	0.7938	0.094
39DAP/reference	0.7955	0.02
41DAP/reference	0.89218	0.153
42DAP/reference	1.09284	0.686
43DAP/reference	1.05695	0.746
47DAP/reference	1.08249	0.324
52DAP/reference	1.03297	1
57DAP/reference	0.75668	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00034	0.786
17DAP/reference	1.01883	1
27DAP/reference	1.1138	0.834
39DAP/reference	0.88456	0.221
41DAP/reference	0.89086	0.094
42DAP/reference	0.81176	0.055
43DAP/reference	1.09184	0.633
47DAP/reference	0.86773	0.031
52DAP/reference	1.00167	0.713
57DAP/reference	1.06366	0.672

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6745	0.047
17DAP/reference	0.95132	0.519
27DAP/reference	0.81289	0.069
39DAP/reference	0.79043	0.054
41DAP/reference	0.73576	0.03
42DAP/reference	1.10594	0.836
43DAP/reference	0.91898	0.281
47DAP/reference	0.93583	0.357
52DAP/reference	1.30556	0.369
57DAP/reference	0.93802	0.346

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91164	0.89
26DAP/20DAP	0.88037	1
34DAP/26DAP	0.96385	0.972
51DAP/34DAP	1.17746	0.095
52DAP/51DAP	0.75469
53DAP/52DAP	1.1464	0.895
55DAP/53DAP	1.24753	0.185
57DAP/55DAP	0.98492	0.831
62DAP/57DAP	0.92919	0.681
68DAP/62DAP	0.92832	0.769
68DAP/14DAP	0.72519	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	7.68494	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.13042	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.81152	1
Mature Eggplant/Ripe Tomato	0.64815	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07216	0.877
1-1-2/M82	0.93765
12-2/M82	0.84539
12-4/M82	1.67323	1
1-3/M82	0.83018	0.441
2-1-1/M82	1.04242
2-1/M82	N/A	N/A
2-6/M82	1.22738	0.594
3-2/M82	1.03423	0.463
4-1-1/M82	1.08439	1
4-1/M82	1.30793
4-3-2/M82	0.85788	0.487
4-3/M82	0.85506	0.72
5-3/M82	0.97646	1
6-2/M82	0.88952
6-3/M82	1.02301	1
7-1/M82	N/A	N/A
7-2/M82	1.02096	1
9-3-2/M82	0.88784

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.83161	0.243
IL2-6/WTpooled	1.00129	1
IL7-5/WTpooled	1.4377	0.792
IL7-3/WTpooled	0.85882	0.31
IL12-4/WTpooled	0.86519	0.71
IL1-4/WTpooled	1.00979	1
WT/WTpooled	1.04646	0.874

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	0.75762	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95283	1
DC3000/delta hrp 6h	1.24743	1
DC3000/delta hrp 12h	1.12956	1
DC3000/delta hrp 24h	0.9376	0.618

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22187	0.094
DC3000 delta B/DC3000 delta AB	0.98699	0.983

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97722	1
Exp 36h	1.19705	0.693
Exp 60h	1.14121	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02815	1
Var 0h	0.92721	0.311
Var 12h I row2-row1	1.23748	0.379
Var 12h NI row2-row1	0.90427	0.627
Var 36h I row2-row1	0.91031	1
Var 36h NI row2-row1	1.64527	1
Var 60h I row2-row1	1.01897	1
Var 60h NI row2-row1	1.10683	0.904
Time course 0hI-0hNI	0.91148	0.185
Time course 12hI-12hNI	1.16704	0.062
Time course 36hI-36hNI	1.01026	0.799
Time course 60hI-60hNI	0.80958	0.047

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)	0.98457	0.789
transgenic ySAMdc/azygous control (breaker)	0.83275	0.173
transgenic ySAMdc/azygous control (red)	0.81849	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99576	0.806

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08496	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.82938	0.172
Manapal/WT (break)	0.91912	1
Manapal/WT (red)	0.98421	0.863