Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.15.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10511	0.904
27DAP/17DAP	0.93347	0.879
39DAP/27DAP	1.0282	1
41DAP/39DAP	0.83937	0.409
42DAP/41DAP	1.12797	0.899
43DAP/42DAP	1.03068	1
47DAP/43DAP	1.0844	0.733
52DAP/47DAP	1.1365	0.767
57DAP/52DAP	0.83412	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31191	0.009
17DAP/reference	0.82329	0.038
27DAP/reference	1.0058	1
39DAP/reference	0.88089	0.221
41DAP/reference	0.78247	0.012
42DAP/reference	1.5591	0.001
43DAP/reference	0.93993	0.464
47DAP/reference	0.89847	0.032
52DAP/reference	0.9429	0.319
57DAP/reference	1.03845	0.704

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94925	0.629
27DAP/17DAP	0.96284	0.887
39DAP/27DAP	1.05963	0.654
41DAP/39DAP	1.04631	0.705
42DAP/41DAP	0.94381	0.541
43DAP/42DAP	0.97801	0.709
47DAP/43DAP	0.97763	0.886
52DAP/47DAP	1.19512	0.414
57DAP/52DAP	1.36936	0.048
57DAP/7DAP	1.45778	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70533	0.091
17DAP/reference	0.89429	0.144
27DAP/reference	0.80514	0.01
39DAP/reference	0.81919	0.025
41DAP/reference	0.91472	0.166
42DAP/reference	1.12154	0.534
43DAP/reference	1.82854	0.034
47DAP/reference	0.70704	0.066
52DAP/reference	0.72993	0.013
57DAP/reference	1.29886	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9365	0.426
17DAP/reference	0.90606	0.032
27DAP/reference	0.91291	0.139
39DAP/reference	0.84602	0.147
41DAP/reference	1.01919	0.683
42DAP/reference	0.97342	0.534
43DAP/reference	1.12086	0.226
47DAP/reference	0.95191	0.184
52DAP/reference	0.84972	0.047
57DAP/reference	0.90753	0.085

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.73041	0.038
17DAP/reference	0.90142	0.381
27DAP/reference	0.8108	0.045
39DAP/reference	0.97368	0.544
41DAP/reference	0.87673	0.148
42DAP/reference	0.8728	0.172
43DAP/reference	1.0926	0.555
47DAP/reference	0.96046	0.434
52DAP/reference	1.84239	0.03
57DAP/reference	1.65799	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94397	1
26DAP/20DAP	1.07442	1
34DAP/26DAP	1.59832	1
51DAP/34DAP	0.94582	0.722
52DAP/51DAP	1.69004	0.034
53DAP/52DAP	0.82276	0.101
55DAP/53DAP	1.31857	0.054
57DAP/55DAP	0.73359	0.118
62DAP/57DAP	1.15172	0.445
68DAP/62DAP	1.43115	0.657
68DAP/14DAP	0.75048	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74883	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.84948	0.347
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.07122	0.224
Mature Eggplant/Ripe Tomato	0.09851	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.16213
12-2/M82	N/A	N/A
12-4/M82	1.05615
1-3/M82	0.90199
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.46984
3-2/M82	0.81119
4-1-1/M82	N/A	N/A
4-1/M82	1.04865
4-3-2/M82	N/A	N/A
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	0.66038
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.37867	0.243
IL2-6/WTpooled	1.17107	0.659
IL7-5/WTpooled	0.62521	1
IL7-3/WTpooled	0.82427	0.418
IL12-4/WTpooled	0.89526	0.581
IL1-4/WTpooled	0.70736	0.394
WT/WTpooled	0.97775	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	0.85862	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11964	0.921
DC3000/delta hrp 6h	2.23862
DC3000/delta hrp 12h	0.99669	1
DC3000/delta hrp 24h	1.12943	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14244	0.384
DC3000 delta B/DC3000 delta AB	0.99038	1

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	0.9777	1
Var 0h	0.99846	1
Var 12h I row2-row1	0.90204	0.363
Var 12h NI row2-row1	0.88019	0.494
Var 36h I row2-row1	1.16612	0.908
Var 36h NI row2-row1	1.26314	1
Var 60h I row2-row1	0.97783	1
Var 60h NI row2-row1	1.00409	1
Time course 0hI-0hNI	1.06063	0.719
Time course 12hI-12hNI	1.00163	1
Time course 36hI-36hNI	1.11022	0.316
Time course 60hI-60hNI	0.79192	0.026

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)	4.62019	0.246
transgenic ySAMdc/azygous control (breaker)	0.56034	0.251
transgenic ySAMdc/azygous control (red)	1.84516	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97166	0.122

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.4192	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.6016	1
Manapal/WT (break)	1.73425	1
Manapal/WT (red)	0.78554	0.36