Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.17.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99387	0.858
27DAP/17DAP	1.31399	0.825
39DAP/27DAP	0.74377	0.402
41DAP/39DAP	0.97578	0.857
42DAP/41DAP	0.89168	1
43DAP/42DAP	1.02897	0.937
47DAP/43DAP	0.93376	0.576
52DAP/47DAP	1.39053	0.597
57DAP/52DAP	2.22785	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11146	0.756
17DAP/reference	1.45025	0.04
27DAP/reference	1.12109	0.291
39DAP/reference	1.32475	0.077
41DAP/reference	1.20163	0.133
42DAP/reference	1.07144	0.842
43DAP/reference	1.14372	0.495
47DAP/reference	1.23814	0.075
52DAP/reference	1.16211	0.388
57DAP/reference	0.91879	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86654	0.402
27DAP/17DAP	0.98437	0.919
39DAP/27DAP	1.20769	0.436
41DAP/39DAP	1.09752	0.887
42DAP/41DAP	1.85587	0.106
43DAP/42DAP	1.64255	0.147
47DAP/43DAP	1.006	1
52DAP/47DAP	1.45502	0.374
57DAP/52DAP	1.02211	1
57DAP/7DAP	0.99404	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82885	0.108
17DAP/reference	0.86608	0.082
27DAP/reference	0.87029	0.076
39DAP/reference	0.77152	0.064
41DAP/reference	0.85525	0.174
42DAP/reference	0.90228	0.2
43DAP/reference	0.84853	0.21
47DAP/reference	0.69665	0.066
52DAP/reference	0.87011	0.15
57DAP/reference	0.77082	0.041

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.57236	0.17
17DAP/reference	0.98253	0.594
27DAP/reference	0.88046	0.327
39DAP/reference	1.06255	0.848
41DAP/reference	0.85458	0.16
42DAP/reference	1.09484	1
43DAP/reference	0.80414	0.054
47DAP/reference	0.98331	0.543
52DAP/reference	1.00038	0.5
57DAP/reference	1.00254	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.72737	0.074
17DAP/reference	0.95054	0.601
27DAP/reference	1.15732	0.552
39DAP/reference	0.94299	0.222
41DAP/reference	0.77472	0.064
42DAP/reference	1.12059	0.424
43DAP/reference	0.99184	0.59
47DAP/reference	1.09518	1
52DAP/reference	1.83742	0.161
57DAP/reference	1.02829	0.753

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.42105	0.733
26DAP/20DAP	1.04798	1
34DAP/26DAP	1.18014	1
51DAP/34DAP	1.20154	0.911
52DAP/51DAP	1.55907
53DAP/52DAP	0.95772	0.79
55DAP/53DAP	0.84796	0.445
57DAP/55DAP	1.53235	0.764
62DAP/57DAP	0.86058	0.681
68DAP/62DAP	0.93367	0.834
68DAP/14DAP	0.40244

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.17409	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.39814	0.226
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.1393
Mature Eggplant/Ripe Tomato	0.3489

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	0.80665	0.619
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	1.08988
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	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.06415	1
IL12-4/WTpooled	1.28416	0.516
IL1-4/WTpooled	1.16081	1
WT/WTpooled	0.96778	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	0.85028	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.22342	0.894
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.00552	1
DC3000/delta hrp 24h	1.02322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.11235	1
Var 0h	0.98373	1
Var 12h I row2-row1	2.43698	0.613
Var 12h NI row2-row1	1.70917	1
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	0.48803	0.743
Var 60h I row2-row1	1.09412	1
Var 60h NI row2-row1	1.04033	1
Time course 0hI-0hNI	0.94407	1
Time course 12hI-12hNI	1.21044	1
Time course 36hI-36hNI	0.66567	0.048
Time course 60hI-60hNI	0.53523	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.35736	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.4273	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)	0.99878	1
Manapal/WT (red)	1.29204	0.413