Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.9.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96362	0.76
27DAP/17DAP	1.32738	0.766
39DAP/27DAP	2.44689	0.042
41DAP/39DAP	1.22508	0.691
42DAP/41DAP	1.10316	0.908
43DAP/42DAP	1.2034	0.793
47DAP/43DAP	1.26964	0.444
52DAP/47DAP	0.81783	0.534
57DAP/52DAP	1.84227	0.427

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56616	0.024
17DAP/reference	0.57939	0.008
27DAP/reference	0.69781	0.083
39DAP/reference	1.15363	1
41DAP/reference	0.85276	0.154
42DAP/reference	1.38516	0.002
43DAP/reference	1.29337	0.01
47DAP/reference	2.30187	0.001
52DAP/reference	1.4876	0.016
57DAP/reference	1.91632	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98097	0.732
27DAP/17DAP	1.12024	0.61
39DAP/27DAP	1.08558	0.512
41DAP/39DAP	0.86935	0.201
42DAP/41DAP	1.06117	0.559
43DAP/42DAP	1.03545	0.585
47DAP/43DAP	1.11885	0.044
52DAP/47DAP	0.97061	0.884
57DAP/52DAP	1.07464	0.679
57DAP/7DAP	1.39248	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84304	0.224
17DAP/reference	0.85105	0.108
27DAP/reference	1.01325	1
39DAP/reference	1.3502	0.086
41DAP/reference	1.86854	0.009
42DAP/reference	1.69642	0.018
43DAP/reference	1.24731	0.024
47DAP/reference	1.29048	0.044
52DAP/reference	1.95681	0.007
57DAP/reference	2.80049	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.44438	0.006
17DAP/reference	0.46575	0.004
27DAP/reference	0.91417	0.34
39DAP/reference	0.8349	0.085
41DAP/reference	1.07212	0.688
42DAP/reference	1.10663	0.509
43DAP/reference	1.2248	0.681
47DAP/reference	3.63482	0.008
52DAP/reference	1.28221	0.009
57DAP/reference	1.82446	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81322	0.098
17DAP/reference	0.74919	0.109
27DAP/reference	1.04538	0.805
39DAP/reference	1.40402	0.016
41DAP/reference	1.09186	0.674
42DAP/reference	1.28541	0.294
43DAP/reference	1.41814	0.081
47DAP/reference	3.15998	0.005
52DAP/reference	3.05506	0.028
57DAP/reference	1.56767	0.104

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94057	1
26DAP/20DAP	1.11028	0.493
34DAP/26DAP	1.06114	1
51DAP/34DAP	1.74464	0.044
52DAP/51DAP	0.86365	0.151
53DAP/52DAP	1.07261	0.797
55DAP/53DAP	0.91197	0.417
57DAP/55DAP	0.95712	0.799
62DAP/57DAP	2.00432	0.015
68DAP/62DAP	1.22874	0.767
68DAP/14DAP	2.29764	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9421	0.239

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.02342	0.036
Mature Green Tomato/Ripe Tomato	0.46262	0.04
Immature Eggplant/Mature Eggplant	29.3383	0.05
Ripe Pepper/Ripe Tomato	2.099	0.258
Mature Eggplant/Ripe Tomato	0.52822	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99822	1
1-1-2/M82	1.42451	1
12-2/M82	1.15547	0.448
12-4/M82	0.8317	0.619
1-3/M82	5.32624
2-1-1/M82	0.91811	1
2-1/M82	0.92152	0.325
2-6/M82	1.32758	0.329
3-2/M82	1.18511	0.717
4-1-1/M82	2.15507	1
4-1/M82	2.38358	1
4-3-2/M82	2.33114	0.241
4-3/M82	1.33813	0.268
5-3/M82	0.41896	0.419
6-2/M82	N/A	N/A
6-3/M82	0.94127	1
7-1/M82	0.85166	0.509
7-2/M82	3.22632	0.324
9-3-2/M82	2.41077	0.171

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.42895	0.277
IL2-6/WTpooled	1.13893	0.659
IL7-5/WTpooled	0.9368	1
IL7-3/WTpooled	1.19577	1
IL12-4/WTpooled	1.12797	0.538
IL1-4/WTpooled	1.10165	1
WT/WTpooled	0.98788	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	1.25347	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.98774	0.95
DC3000/delta hrp 12h	1.1153	1
DC3000/delta hrp 24h	1.02443	0.769

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.01115	1
DC3000 delta B/DC3000 delta AB	1.24779	0.151

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11606	1
Exp 36h	1.10386	1
Exp 60h	1.09036	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02195	1
Var 0h	1.36437	0.782
Var 12h I row2-row1	0.88982	0.514
Var 12h NI row2-row1	1.10132	1
Var 36h I row2-row1	1.03591	1
Var 36h NI row2-row1	0.82932	0.522
Var 60h I row2-row1	0.61711	0.285
Var 60h NI row2-row1	0.89505	0.408
Time course 0hI-0hNI	1.04997	0.218
Time course 12hI-12hNI	1.06273	0.56
Time course 36hI-36hNI	1.80687	0.006
Time course 60hI-60hNI	4.55899	0.008

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)	0.55093	0.314
transgenic ySAMdc/azygous control (breaker)	0.91868	0.49
transgenic ySAMdc/azygous control (red)	1.10344	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.81215	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82086	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.83357	0.093
Manapal/WT (break)	4.84249	0.183
Manapal/WT (red)	1.8462	0.164