Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82214	0.182
27DAP/17DAP	0.95359	0.945
39DAP/27DAP	0.95889	0.652
41DAP/39DAP	1.23645	0.569
42DAP/41DAP	1.11956	0.908
43DAP/42DAP	1.01456	0.937
47DAP/43DAP	1.0537	0.95
52DAP/47DAP	1.42611	0.31
57DAP/52DAP	0.94843	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77142	0.026
17DAP/reference	0.78312	0.008
27DAP/reference	0.84866	0.114
39DAP/reference	0.90052	0.042
41DAP/reference	0.79159	0.018
42DAP/reference	0.91107	0.038
43DAP/reference	0.85272	0.023
47DAP/reference	0.93341	0.191
52DAP/reference	1.09352	0.242
57DAP/reference	1.20728	0.032

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24223	0.492
27DAP/17DAP	1.11331	0.523
39DAP/27DAP	1.07426	0.845
41DAP/39DAP	1.15019	0.799
42DAP/41DAP	0.63462	0.053
43DAP/42DAP	1.24089	0.746
47DAP/43DAP	1.05785	0.822
52DAP/47DAP	0.95448	0.925
57DAP/52DAP	1.20248	0.376
57DAP/7DAP	0.78868	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90943	0.168
17DAP/reference	0.74873	0.012
27DAP/reference	0.78735	0.011
39DAP/reference	0.85243	0.025
41DAP/reference	0.80888	0.017
42DAP/reference	0.82983	0.017
43DAP/reference	0.80038	0.026
47DAP/reference	0.85855	0.128
52DAP/reference	0.93896	0.254
57DAP/reference	0.94077	0.223

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81055	0.043
17DAP/reference	0.61683	0.004
27DAP/reference	0.8199	0.032
39DAP/reference	0.80209	0.038
41DAP/reference	1.02966	1
42DAP/reference	0.93964	0.212
43DAP/reference	0.83175	0.128
47DAP/reference	0.77015	0.194
52DAP/reference	0.86543	0.066
57DAP/reference	0.64548	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89411	0.092
17DAP/reference	0.8235	0.103
27DAP/reference	0.73758	0.039
39DAP/reference	0.81168	0.046
41DAP/reference	0.79874	0.026
42DAP/reference	0.77827	0.02
43DAP/reference	0.82643	0.039
47DAP/reference	0.90738	0.215
52DAP/reference	0.62607	0.102
57DAP/reference	0.96499	0.483

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.23899	0.817
26DAP/20DAP	1.06726	1
34DAP/26DAP	0.89209	0.879
51DAP/34DAP	1.00137	0.893
52DAP/51DAP	1.27779	0.454
53DAP/52DAP	0.97691	0.902
55DAP/53DAP	1.38628	0.589
57DAP/55DAP	0.68448	0.309
62DAP/57DAP	0.90654	0.871
68DAP/62DAP	1.24284	0.491
68DAP/14DAP	1.03774	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73303	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.81692
Mature Green Tomato/Ripe Tomato	0.7168	0.165
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.20186

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.93339
12-2/M82	N/A	N/A
12-4/M82	1.20707	0.694
1-3/M82	0.60379
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	1.06687	1
4-3-2/M82	1.021	0.284
4-3/M82	N/A	N/A
5-3/M82	0.84399	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.98752
9-3-2/M82	0.93704

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.21281	0.277
IL2-6/WTpooled	0.72723	0.348
IL7-5/WTpooled	0.92173	1
IL7-3/WTpooled	1.38743	1
IL12-4/WTpooled	1.27262	0.646
IL1-4/WTpooled	0.92077	0.834
WT/WTpooled	1.03514	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	1.05392	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03582	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.99029	1
DC3000/delta hrp 24h	0.96147	0.782

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	0.90932	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02177	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.20074	0.736
Var 12h NI row2-row1	1.47336	0.649
Var 36h I row2-row1	1.11539	0.601
Var 36h NI row2-row1	0.67341	1
Var 60h I row2-row1	1.02425	0.562
Var 60h NI row2-row1	1.20774	0.904
Time course 0hI-0hNI	1.11866	0.852
Time course 12hI-12hNI	1.15992	0.085
Time course 36hI-36hNI	2.05569	0.006
Time course 60hI-60hNI	1.47126	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)	2.55589	0.235
transgenic ySAMdc/azygous control (breaker)	1.2028	0.248
transgenic ySAMdc/azygous control (red)	1.41228	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02075	0.421

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88532	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37326	0.14
Manapal/WT (break)	0.9838	1
Manapal/WT (red)	1.26137	1