Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.12.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02588	0.927
27DAP/17DAP	0.97575	0.952
39DAP/27DAP	1.03043	0.857
41DAP/39DAP	0.97483	0.915
42DAP/41DAP	1.2254	0.877
43DAP/42DAP	0.95292	0.906
47DAP/43DAP	0.97705	0.902
52DAP/47DAP	1.08832	0.95
57DAP/52DAP	0.97035	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0016	0.806
17DAP/reference	0.9749	0.63
27DAP/reference	0.97208	0.514
39DAP/reference	1.20672	0.093
41DAP/reference	1.04375	0.552
42DAP/reference	1.03687	0.756
43DAP/reference	1.1018	0.705
47DAP/reference	1.20276	0.001
52DAP/reference	1.12181	0.108
57DAP/reference	1.21053	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06116	1
27DAP/17DAP	0.95699	0.854
39DAP/27DAP	1.00591	0.977
41DAP/39DAP	0.91364	0.729
42DAP/41DAP	1.26614	0.354
43DAP/42DAP	1.50281	0.017
47DAP/43DAP	0.954	0.677
52DAP/47DAP	1.22798	0.414
57DAP/52DAP	0.88641	0.428
57DAP/7DAP	1.74396	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10562	0.119
17DAP/reference	1.22654	0.013
27DAP/reference	1.17168	0.02
39DAP/reference	1.21018	0.023
41DAP/reference	1.34936	0.015
42DAP/reference	1.47366	0.007
43DAP/reference	1.4343	0.012
47DAP/reference	1.13876	0.36
52DAP/reference	1.24729	0.197
57DAP/reference	1.12548	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03391	0.863
17DAP/reference	1.50233	0.32
27DAP/reference	1.00383	0.735
39DAP/reference	1.11665	0.783
41DAP/reference	0.85356	0.112
42DAP/reference	1.01682	1
43DAP/reference	1.46279	0.09
47DAP/reference	0.98481	0.559
52DAP/reference	0.92877	0.327
57DAP/reference	1.22091	0.182

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11431	0.311
17DAP/reference	1.26287	0.096
27DAP/reference	1.41657	0.023
39DAP/reference	1.28529	0.022
41DAP/reference	1.25365	0.02
42DAP/reference	1.34298	0.017
43DAP/reference	1.08552	0.375
47DAP/reference	1.26643	0.048
52DAP/reference	1.52627	0.049
57DAP/reference	0.92285	0.171

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05583	1
26DAP/20DAP	1.00737	1
34DAP/26DAP	1.19896	1
51DAP/34DAP	1.19968	0.207
52DAP/51DAP	1.17462	0.396
53DAP/52DAP	1.23854	0.113
55DAP/53DAP	0.99914	0.939
57DAP/55DAP	1.18461	0.915
62DAP/57DAP	0.73753	0.28
68DAP/62DAP	1.11832	0.907
68DAP/14DAP	0.97445	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.61166	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.04987	0.805
Mature Green Tomato/Ripe Tomato	0.54747
Immature Eggplant/Mature Eggplant	0.99396	1
Ripe Pepper/Ripe Tomato	0.51673	0.224
Mature Eggplant/Ripe Tomato	0.33274	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04446	0.536
1-1-2/M82	1.03615	1
12-2/M82	0.79657
12-4/M82	1.01573	1
1-3/M82	0.74213
2-1-1/M82	1.1938	0.764
2-1/M82	0.81931	0.74
2-6/M82	1.08784	0.374
3-2/M82	0.5931
4-1-1/M82	0.82956	1
4-1/M82	2.28355	1
4-3-2/M82	0.94758
4-3/M82	1.24472	1
5-3/M82	0.82322	0.395
6-2/M82	N/A	N/A
6-3/M82	0.93275	1
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.23785	0.441
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.18902	1
IL12-4/WTpooled	1.04	0.737
IL1-4/WTpooled	1.38085	1
WT/WTpooled	0.98065	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	0.9349	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03469	0.921
DC3000/delta hrp 6h	0.75194	0.874
DC3000/delta hrp 12h	1.00502	1
DC3000/delta hrp 24h	1.0212	0.797

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	0.85685	0.406
Exp 60h	0.99567	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05877	1
Var 0h	0.68461	0.332
Var 12h I row2-row1	1.06082	0.736
Var 12h NI row2-row1	0.97608	0.82
Var 36h I row2-row1	0.79972	1
Var 36h NI row2-row1	1.00173	1
Var 60h I row2-row1	2.09658	1
Var 60h NI row2-row1	0.9073	0.866
Time course 0hI-0hNI	1.04639	0.799
Time course 12hI-12hNI	0.97446	0.858
Time course 36hI-36hNI	0.99636	0.742
Time course 60hI-60hNI	1.09461	0.216

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)	1.19011	0.268
transgenic ySAMdc/azygous control (breaker)	0.63976	0.173
transgenic ySAMdc/azygous control (red)	0.75282	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99045	0.517

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7492	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8533	1
Manapal/WT (break)	1.02995	1
Manapal/WT (red)	1.10861	0.222