Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10542	0.588
27DAP/17DAP	1.11665	0.854
39DAP/27DAP	1.04909	0.974
41DAP/39DAP	1.00596	1
42DAP/41DAP	1.11982	0.882
43DAP/42DAP	1.06852	0.985
47DAP/43DAP	1.28078	0.442
52DAP/47DAP	0.88373	0.67
57DAP/52DAP	1.06046	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10291	0.806
17DAP/reference	0.50825	0.007
27DAP/reference	0.85724	0.257
39DAP/reference	0.72738	0.076
41DAP/reference	0.37627	0.008
42DAP/reference	1.1857	0.093
43DAP/reference	0.76803	0.026
47DAP/reference	1.17542	0.101
52DAP/reference	2.30979	0.016
57DAP/reference	1.55852	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0443	0.736
27DAP/17DAP	0.90047	0.39
39DAP/27DAP	1.04687	0.626
41DAP/39DAP	0.85912	0.265
42DAP/41DAP	1.22317	0.029
43DAP/42DAP	1.10092	0.162
47DAP/43DAP	0.91885	0.428
52DAP/47DAP	1.50418	0.167
57DAP/52DAP	1.63145	0.059
57DAP/7DAP	1.49816	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16796
17DAP/reference	2.15669	0.026
27DAP/reference	2.30121	0.006
39DAP/reference	N/A	N/A
41DAP/reference	1.96263
42DAP/reference	N/A	N/A
43DAP/reference	4.04858	0.006
47DAP/reference	3.03296	0.272
52DAP/reference	2.63577	0.007
57DAP/reference	2.71671	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94974	0.77
17DAP/reference	0.99513	0.805
27DAP/reference	1.62911	0.516
39DAP/reference	1.09245	0.112
41DAP/reference	0.77879
42DAP/reference	1.01602	1
43DAP/reference	0.67593	0.006
47DAP/reference	0.76568	0.087
52DAP/reference	1.64286	0.006
57DAP/reference	1.212	0.494

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67112
17DAP/reference	1.40747	0.81
27DAP/reference	3.84971	0.031
39DAP/reference	0.84188	0.046
41DAP/reference	2.75691	0.007
42DAP/reference	N/A	N/A
43DAP/reference	3.61496	0.006
47DAP/reference	1.17977	0.754
52DAP/reference	2.12094	0.443
57DAP/reference	N/A	N/A

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23831	0.966
26DAP/20DAP	0.99149	1
34DAP/26DAP	1.54888	1
51DAP/34DAP	1.18813	0.666
52DAP/51DAP	2.63038	0.039
53DAP/52DAP	0.67477	0.049
55DAP/53DAP	1.30128	0.039
57DAP/55DAP	0.26925	0.016
62DAP/57DAP	1.72336	0.133
68DAP/62DAP	7.704	0.028
68DAP/14DAP	11.1242	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.49196	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.76734	0.079
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.03181
Mature Eggplant/Ripe Tomato	0.86482	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95764	0.944
1-1-2/M82	1.04847	1
12-2/M82	1.00457	1
12-4/M82	1.15718	1
1-3/M82	0.96778	1
2-1-1/M82	1.18621	0.764
2-1/M82	1.40177	1
2-6/M82	0.94804	1
3-2/M82	1.00785	1
4-1-1/M82	0.9805	1
4-1/M82	0.97234
4-3-2/M82	1.19626	1
4-3/M82	1.04256	0.268
5-3/M82	0.99799	1
6-2/M82	0.98029	1
6-3/M82	1.0008	1
7-1/M82	1.01986	1
7-2/M82	0.99045	1
9-3-2/M82	1.22797	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06047
IL2-6/WTpooled	0.96525	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01271	1
IL12-4/WTpooled	0.9649	0.543
IL1-4/WTpooled	0.93252
WT/WTpooled	1.00454	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	1.17404	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02867	0.921
DC3000/delta hrp 6h	0.88999	0.95
DC3000/delta hrp 12h	0.52712	1
DC3000/delta hrp 24h	1.02185	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.32483	0.042
DC3000 delta B/DC3000 delta AB	1.31257	0.274

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	0.98547	1
Var 0h	0.46334	0.261
Var 12h I row2-row1	0.84261	0.39
Var 12h NI row2-row1	1.03393	1
Var 36h I row2-row1	1.35036	0.601
Var 36h NI row2-row1	1.06524	1
Var 60h I row2-row1	0.7891
Var 60h NI row2-row1	0.88228	0.977
Time course 0hI-0hNI	0.92056	0.415
Time course 12hI-12hNI	1.0219	0.885
Time course 36hI-36hNI	1.02577	0.975
Time course 60hI-60hNI	1.06489	0.426

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)	0.83349	0.291
transgenic ySAMdc/azygous control (breaker)	0.80612	0.173
transgenic ySAMdc/azygous control (red)	1.57247	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03456	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94712	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05518	0.307
Manapal/WT (break)	1.45897	0.183
Manapal/WT (red)	1.02795	1