Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06512	0.961
27DAP/17DAP	1.11785	0.857
39DAP/27DAP	0.90066	0.544
41DAP/39DAP	1.11105	0.685
42DAP/41DAP	1.03386	0.994
43DAP/42DAP	1.01181	0.937
47DAP/43DAP	1.16085	0.442
52DAP/47DAP	0.99065	0.924
57DAP/52DAP	1.01984	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9352	0.14
17DAP/reference	0.94625	0.419
27DAP/reference	0.96743	0.581
39DAP/reference	0.79712	0.039
41DAP/reference	0.93983	0.434
42DAP/reference	0.88004	0.017
43DAP/reference	1.02321	0.866
47DAP/reference	0.97345	0.418
52DAP/reference	0.94452	0.283
57DAP/reference	0.96009	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.83393	0.132
27DAP/17DAP	1.16542	0.658
39DAP/27DAP	0.95467	0.737
41DAP/39DAP	1.19943	0.514
42DAP/41DAP	0.90302	0.384
43DAP/42DAP	0.92037	0.466
47DAP/43DAP	1.02653	1
52DAP/47DAP	0.91012	0.671
57DAP/52DAP	1.28354	0.289
57DAP/7DAP	1.40678	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91963	0.326
17DAP/reference	0.95824	0.389
27DAP/reference	0.98741	0.53
39DAP/reference	1.07433	1
41DAP/reference	0.91445	0.341
42DAP/reference	0.91212	0.082
43DAP/reference	0.94895	0.279
47DAP/reference	0.74607	0.057
52DAP/reference	1.10009	0.375
57DAP/reference	0.97874	0.513

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95664	0.592
17DAP/reference	1.07668	0.898
27DAP/reference	0.86959	0.144
39DAP/reference	0.90432	0.257
41DAP/reference	0.81781	0.07
42DAP/reference	0.83881	0.169
43DAP/reference	0.9774	0.569
47DAP/reference	0.7773	0.053
52DAP/reference	0.97379	0.469
57DAP/reference	0.94936	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15076	0.32
17DAP/reference	0.94833	0.592
27DAP/reference	0.95306	0.539
39DAP/reference	1.01509	0.987
41DAP/reference	1.13476	0.521
42DAP/reference	1.23259	0.158
43DAP/reference	1.13557	0.755
47DAP/reference	0.8572	0.125
52DAP/reference	1.03667	0.928
57DAP/reference	0.95993	0.516

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09202	0.966
26DAP/20DAP	0.80828	0.512
34DAP/26DAP	1.03259	1
51DAP/34DAP	1.69932	0.039
52DAP/51DAP	1.10398	0.848
53DAP/52DAP	1.18718	0.428
55DAP/53DAP	0.99916	0.886
57DAP/55DAP	0.95107	0.783
62DAP/57DAP	0.81124	0.088
68DAP/62DAP	0.95665	0.885
68DAP/14DAP	1.25158	0.08

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.65001	0.05

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.10625	0.814
Immature Eggplant/Mature Eggplant	47.4714
Ripe Pepper/Ripe Tomato	2.49262
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.94252
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	1.09795
4-1-1/M82	N/A	N/A
4-1/M82	0.95001
4-3-2/M82	1.00373	1
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	0.95168	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92763
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.0675
IL12-4/WTpooled	0.79912	0.71
IL1-4/WTpooled	1.08526
WT/WTpooled	1.13275	0.785

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	1.05138	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98036	1
DC3000/delta hrp 6h	1.05605	1
DC3000/delta hrp 12h	1.03455	1
DC3000/delta hrp 24h	0.76248	0.071

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	0.56347	1
Exp 36h	0.8842	0.82
Exp 60h	0.87393	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.25767	1
Var 0h	0.92877	0.933
Var 12h I row2-row1	1.0016	1
Var 12h NI row2-row1	0.68534	0.649
Var 36h I row2-row1	0.96795	0.438
Var 36h NI row2-row1	0.73163	0.272
Var 60h I row2-row1	0.97081	0.832
Var 60h NI row2-row1	0.49461	0.516
Time course 0hI-0hNI	0.95939	0.833
Time course 12hI-12hNI	0.94581	0.776
Time course 36hI-36hNI	0.85161	0.029
Time course 60hI-60hNI	1.21708	0.012

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)	1.2312	0.271
transgenic ySAMdc/azygous control (breaker)	1.9486	0.178
transgenic ySAMdc/azygous control (red)	1.70489	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05362	0.185

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40981	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.47889	0.087
Manapal/WT (break)	2.02282	0.13
Manapal/WT (red)	1.49326	0.413