Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.14.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25374	0.428
27DAP/17DAP	0.4295	0.027
39DAP/27DAP	0.6921	0.27
41DAP/39DAP	0.66768	0.097
42DAP/41DAP	0.79494	1
43DAP/42DAP	1.32309	0.478
47DAP/43DAP	0.60833	0.086
52DAP/47DAP	1.13166	0.821
57DAP/52DAP	0.96364	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.648	0.031
17DAP/reference	0.55889	0.019
27DAP/reference	0.43765	0.012
39DAP/reference	0.39232	0.01
41DAP/reference	0.28312	0.008
42DAP/reference	0.28835	0.001
43DAP/reference	0.33072	0.013
47DAP/reference	0.27044	0.001
52DAP/reference	0.22653	0.012
57DAP/reference	0.35784	0.007

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.78361	0.036
27DAP/17DAP	0.74443	0.241
39DAP/27DAP	0.44059	0.035
41DAP/39DAP	1.39752	0.197
42DAP/41DAP	0.80535	0.096
43DAP/42DAP	0.61981	0.02
47DAP/43DAP	0.86831	0.247
52DAP/47DAP	0.91123	0.753
57DAP/52DAP	1.13097	0.657
57DAP/7DAP	0.33749	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2485	0.181
17DAP/reference	1.09367	0.147
27DAP/reference	1.35799	0.013
39DAP/reference	1.20476	0.044
41DAP/reference	1.09463	0.709
42DAP/reference	1.14635	0.308
43DAP/reference	1.20307	0.014
47DAP/reference	0.51605	0.101
52DAP/reference	1.3201	0.062
57DAP/reference	1.18519	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43932	0.006
17DAP/reference	0.53422	0.008
27DAP/reference	0.50973	0.009
39DAP/reference	0.29383	0.007
41DAP/reference	0.33511	0.005
42DAP/reference	0.33481	0.01
43DAP/reference	0.36485	0.006
47DAP/reference	0.25093	0.007
52DAP/reference	0.16465	0.003
57DAP/reference	0.13747	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56785	0.016
17DAP/reference	1.38777	0.06
27DAP/reference	1.33684	0.02
39DAP/reference	1.44565	0.342
41DAP/reference	0.97322	0.618
42DAP/reference	1.02128	0.816
43DAP/reference	0.81739	0.206
47DAP/reference	0.27479	0.004
52DAP/reference	0.8794	0.327
57DAP/reference	0.76951	0.068

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08383	1
26DAP/20DAP	0.97042	1
34DAP/26DAP	0.7671	0.399
51DAP/34DAP	0.42642	0.049
52DAP/51DAP	1.06576	0.776
53DAP/52DAP	0.63947	0.049
55DAP/53DAP	0.79918	0.203
57DAP/55DAP	1.22198	0.935
62DAP/57DAP	1.47403	0.133
68DAP/62DAP	0.82307	0.641
68DAP/14DAP	0.35897	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.46713	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.87786	0.058
Mature Green Tomato/Ripe Tomato	6.40355	0.015
Immature Eggplant/Mature Eggplant	0.50887	0.058
Ripe Pepper/Ripe Tomato	2.861	0.258
Mature Eggplant/Ripe Tomato	4.71117	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.65697
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	1.4276
5-3/M82	1.43816	0.455
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.29733
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.41712	0.277
IL2-6/WTpooled	0.76471	0.348
IL7-5/WTpooled	1.21969	0.792
IL7-3/WTpooled	1.13532	1
IL12-4/WTpooled	0.93907	1
IL1-4/WTpooled	1.04686	1
WT/WTpooled	1.01427	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	1.03241	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94691	1
DC3000/delta hrp 6h	1.01253	1
DC3000/delta hrp 12h	1.0586	1
DC3000/delta hrp 24h	1.01282	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82942	0.597
DC3000 delta B/DC3000 delta AB	0.57046	0.027

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0011	1
Exp 36h	1.03903	0.693
Exp 60h	0.94172	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.004	1
Var 0h	0.55261	0.782
Var 12h I row2-row1	0.96539	0.77
Var 12h NI row2-row1	1.01397	1
Var 36h I row2-row1	0.98194	1
Var 36h NI row2-row1	1.04233	1
Var 60h I row2-row1	1.57742	0.562
Var 60h NI row2-row1	0.96345	0.69
Time course 0hI-0hNI	0.96292	0.799
Time course 12hI-12hNI	1.0719	0.621
Time course 36hI-36hNI	1.01057	0.841
Time course 60hI-60hNI	0.33254	0.007

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)	1.10229	0.455
transgenic ySAMdc/azygous control (breaker)	1.73836	0.162
transgenic ySAMdc/azygous control (red)	1.02601	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.50299	0.09

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40334	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.65645	0.087
Manapal/WT (break)	2.93241	0.123
Manapal/WT (red)	1.14979	1