Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02888	0.997
27DAP/17DAP	1.07616	0.88
39DAP/27DAP	1.10601	0.864
41DAP/39DAP	0.62899	0.068
42DAP/41DAP	1.1608	0.938
43DAP/42DAP	1.01575	1
47DAP/43DAP	0.96279	0.828
52DAP/47DAP	0.99094	0.903
57DAP/52DAP	1.10308	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99957	0.756
17DAP/reference	1.25745	0.011
27DAP/reference	1.00243	0.904
39DAP/reference	1.05279	0.335
41DAP/reference	1.22013	0.016
42DAP/reference	0.90615	0.037
43DAP/reference	1.03704	0.787
47DAP/reference	0.90108	0.06
52DAP/reference	0.81838	0.079
57DAP/reference	0.92386	0.199

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05069	0.749
27DAP/17DAP	1.05125	0.867
39DAP/27DAP	0.99152	0.984
41DAP/39DAP	1.1888	0.59
42DAP/41DAP	1.66154	0.708
43DAP/42DAP	0.92434	0.293
47DAP/43DAP	1.04909	0.939
52DAP/47DAP	0.86442	0.446
57DAP/52DAP	0.9737	0.763
57DAP/7DAP	1.12688	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97425	0.55
17DAP/reference	0.87431	0.025
27DAP/reference	0.76086	0.012
39DAP/reference	0.91387	0.126
41DAP/reference	0.88295	0.103
42DAP/reference	0.91367	0.211
43DAP/reference	0.92632	0.252
47DAP/reference	0.86834	0.101
52DAP/reference	1.06316	1
57DAP/reference	0.90367	0.144

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04382	0.823
17DAP/reference	1.10352	0.139
27DAP/reference	0.87272	0.097
39DAP/reference	0.90836	0.235
41DAP/reference	0.8334	0.054
42DAP/reference	0.81245	0.023
43DAP/reference	1.06321	0.662
47DAP/reference	0.96256	0.338
52DAP/reference	0.93819	0.171
57DAP/reference	1.17765	0.07

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02878	0.939
17DAP/reference	1.00914	0.855
27DAP/reference	0.91945	0.257
39DAP/reference	0.98576	0.591
41DAP/reference	1.36806	0.319
42DAP/reference	0.94067	0.445
43DAP/reference	0.94926	0.432
47DAP/reference	0.95516	0.371
52DAP/reference	0.94354	0.551
57DAP/reference	0.64757	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.89591	0.733
26DAP/20DAP	1.29459	0.134
34DAP/26DAP	1.21624	1
51DAP/34DAP	0.91341	0.618
52DAP/51DAP	0.87945	1
53DAP/52DAP	1.06385	0.921
55DAP/53DAP	0.99387	0.886
57DAP/55DAP	0.95923	0.804
62DAP/57DAP	0.99597	0.994
68DAP/62DAP	0.63637	0.166
68DAP/14DAP	0.72135	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.29574	0.285

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.31975	0.399
Immature Eggplant/Mature Eggplant	1.45678	0.157
Ripe Pepper/Ripe Tomato	0.67566	0.224
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	N/A	N/A
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	1.17566
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
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	0.3472
9-3-2/M82	1.30063

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84712	1
IL2-6/WTpooled	1.24939	0.415
IL7-5/WTpooled	1.49633
IL7-3/WTpooled	0.74957	0.418
IL12-4/WTpooled	0.96306	1
IL1-4/WTpooled	0.51615	0.699
WT/WTpooled	1.03789	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	1.07883	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07209	0.914
DC3000/delta hrp 6h	1.23378	1
DC3000/delta hrp 12h	1.12937	1
DC3000/delta hrp 24h	0.55149	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57747
DC3000 delta B/DC3000 delta AB	0.86961	0.456

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98837	1
Exp 36h	1.17887	0.693
Exp 60h	1.14635	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98132	1
Var 0h	1.33481
Var 12h I row2-row1	1.09059	0.736
Var 12h NI row2-row1	1.43133
Var 36h I row2-row1	1.20286	0.298
Var 36h NI row2-row1	1.49997	1
Var 60h I row2-row1	1.03404
Var 60h NI row2-row1	0.80184	0.292
Time course 0hI-0hNI	0.9114	0.415
Time course 12hI-12hNI	1.1514	0.233
Time course 36hI-36hNI	1.35406	0.128
Time course 60hI-60hNI	1.16941	0.254

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)	0.99774	0.931
transgenic ySAMdc/azygous control (breaker)	1.0743	1
transgenic ySAMdc/azygous control (red)	1.03973	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98316	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99621	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96334	1
Manapal/WT (break)	1.09497	1
Manapal/WT (red)	N/A	N/A