Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98723	0.83
27DAP/17DAP	0.83493	0.597
39DAP/27DAP	0.82704	0.507
41DAP/39DAP	1.03227	1
42DAP/41DAP	0.75628	0.774
43DAP/42DAP	2.15313	0.047
47DAP/43DAP	0.60418	0.107
52DAP/47DAP	1.07425	0.906
57DAP/52DAP	1.00213	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78848	0.025
17DAP/reference	0.91063	0.091
27DAP/reference	1.05384	0.569
39DAP/reference	1.01337	0.828
41DAP/reference	0.85581	0.085
42DAP/reference	0.91379	0.103
43DAP/reference	1.14354	0.152
47DAP/reference	1.07231	0.524
52DAP/reference	1.26102	0.012
57DAP/reference	1.37485	0.026

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25647	0.051
27DAP/17DAP	1.12842	0.658
39DAP/27DAP	0.67085	0.048
41DAP/39DAP	1.12901	0.674
42DAP/41DAP	0.97707	0.759
43DAP/42DAP	0.79341	0.028
47DAP/43DAP	1.09347	0.812
52DAP/47DAP	1.0063	0.982
57DAP/52DAP	1.15738	0.431
57DAP/7DAP	0.68457	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95266	0.246
17DAP/reference	3.32371	0.006
27DAP/reference	2.42255	0.007
39DAP/reference	2.50696	0.006
41DAP/reference	1.52882	0.019
42DAP/reference	1.26834	0.1
43DAP/reference	0.63063	0.015
47DAP/reference	0.95718	0.504
52DAP/reference	0.79756	0.04
57DAP/reference	0.8691	0.041

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95237	0.548
17DAP/reference	0.80969	0.028
27DAP/reference	0.82333	0.056
39DAP/reference	0.93292	0.25
41DAP/reference	0.87331	0.051
42DAP/reference	0.85888	0.022
43DAP/reference	0.86564	0.191
47DAP/reference	0.81933	0.016
52DAP/reference	1.03602	0.747
57DAP/reference	0.83711	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81622	0.119
17DAP/reference	0.96304	0.601
27DAP/reference	1.29201	0.237
39DAP/reference	1.18415	0.227
41DAP/reference	1.0791	0.369
42DAP/reference	1.03108	0.923
43DAP/reference	1.00326	0.767
47DAP/reference	1.02335	1
52DAP/reference	0.89707	0.319
57DAP/reference	1.29589	0.066

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01629	1
26DAP/20DAP	1.18497	0.635
34DAP/26DAP	0.99423	0.961
51DAP/34DAP	0.83953	0.351
52DAP/51DAP	0.87517	1
53DAP/52DAP	1.16016	0.204
55DAP/53DAP	0.81087	0.43
57DAP/55DAP	1.56258	0.543
62DAP/57DAP	1.309	0.029
68DAP/62DAP	1.30091	0.042
68DAP/14DAP	0.99683	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13136	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52607	0.139
Mature Green Tomato/Ripe Tomato	2.25358	0.048
Immature Eggplant/Mature Eggplant	1.79701	0.05
Ripe Pepper/Ripe Tomato	5.39579
Mature Eggplant/Ripe Tomato	1.72783

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.89073	1
12-2/M82	N/A	N/A
12-4/M82	0.88292	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.8257	1
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.82458
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	1.06859	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.51713
7-2/M82	1.08846
9-3-2/M82	0.99613

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.55817
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.67789
IL12-4/WTpooled	0.97909	1
IL1-4/WTpooled	1.3542
WT/WTpooled	1.12413	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	0.87421	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01976	1
DC3000/delta hrp 6h	0.50974	0.95
DC3000/delta hrp 12h	0.97385	1
DC3000/delta hrp 24h	1.15598	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22576	0.441
DC3000 delta B/DC3000 delta AB	0.86769	0.253

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98821	1
Exp 36h	0.96467	0.943
Exp 60h	0.86333	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.14838	1
Var 0h	0.86214	0.933
Var 12h I row2-row1	2.19713	0.544
Var 12h NI row2-row1	0.9403	0.82
Var 36h I row2-row1	1.24576	0.908
Var 36h NI row2-row1	1.09673	1
Var 60h I row2-row1	0.91416	0.832
Var 60h NI row2-row1	0.8869	0.932
Time course 0hI-0hNI	0.90838	0.213
Time course 12hI-12hNI	0.98286	0.906
Time course 36hI-36hNI	0.88288	0.035
Time course 60hI-60hNI	1.00411	1

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)	1.05404	0.372
transgenic ySAMdc/azygous control (breaker)	0.9403	1
transgenic ySAMdc/azygous control (red)	1.13237	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0238	0.395

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.89505	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05331	0.084
Manapal/WT (break)	1.11819	1
Manapal/WT (red)	1.13283	0.137