Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0338	0.722
27DAP/17DAP	0.93189	0.763
39DAP/27DAP	1.61615	0.088
41DAP/39DAP	0.59101	0.045
42DAP/41DAP	0.96847	1
43DAP/42DAP	1.12847	1
47DAP/43DAP	0.52966	0.061
52DAP/47DAP	1.52091	0.338
57DAP/52DAP	1.40879	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06483	0.735
17DAP/reference	1.02546	0.239
27DAP/reference	1.03442	0.648
39DAP/reference	1.03392	0.413
41DAP/reference	1.09797	0.013
42DAP/reference	0.92638	0.045
43DAP/reference	1.00053	0.942
47DAP/reference	0.95702	0.06
52DAP/reference	0.86852	0.147
57DAP/reference	0.82472	0.049

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1661	0.841
27DAP/17DAP	1.05623	0.973
39DAP/27DAP	0.98373	0.852
41DAP/39DAP	1.16261	0.827
42DAP/41DAP	0.85385	0.356
43DAP/42DAP	1.25504	0.273
47DAP/43DAP	0.89783	0.516
52DAP/47DAP	1.0229	0.93
57DAP/52DAP	1.40874	0.376
57DAP/7DAP	1.48399	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82887	0.08
17DAP/reference	0.93954	0.144
27DAP/reference	0.86457	0.014
39DAP/reference	0.93744	0.056
41DAP/reference	0.94343	0.133
42DAP/reference	0.89749	0.019
43DAP/reference	0.93768	0.029
47DAP/reference	0.92661	0.293
52DAP/reference	0.88129	0.017
57DAP/reference	0.90478	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12243	0.149
17DAP/reference	1.06672	0.083
27DAP/reference	0.9308	0.16
39DAP/reference	0.9048	0.132
41DAP/reference	0.97209	0.412
42DAP/reference	0.93457	0.212
43DAP/reference	1.13888	0.429
47DAP/reference	0.91653	0.011
52DAP/reference	1.09086	0.106
57DAP/reference	1.09073	0.048

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99226	0.607
17DAP/reference	1.00931	1
27DAP/reference	0.93731	0.206
39DAP/reference	0.91958	0.046
41DAP/reference	1.01661	1
42DAP/reference	0.89217	0.172
43DAP/reference	0.84617	0.079
47DAP/reference	1.08724	0.115
52DAP/reference	0.92667	0.455
57DAP/reference	0.88396	0.152

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9476	0.997
26DAP/20DAP	1.03064	1
34DAP/26DAP	0.85372	0.777
51DAP/34DAP	0.96338	0.743
52DAP/51DAP	1.21943	0.313
53DAP/52DAP	1.20959	0.783
55DAP/53DAP	1.06455	0.855
57DAP/55DAP	1.26985	0.064
62DAP/57DAP	1.03937	0.902
68DAP/62DAP	1.00656	0.939
68DAP/14DAP	0.97294	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.19518	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.00784
Mature Green Tomato/Ripe Tomato	1.63118	0.015
Immature Eggplant/Mature Eggplant	1.17183	0.3
Ripe Pepper/Ripe Tomato	0.19452	0.224
Mature Eggplant/Ripe Tomato	0.17764

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.31859
12-2/M82	N/A	N/A
12-4/M82	1.49956
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	0.97793
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	0.77482
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.12103
7-2/M82	N/A	N/A
9-3-2/M82	1.48226	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9038	1
IL2-6/WTpooled	1.10023	0.531
IL7-5/WTpooled	3.44248
IL7-3/WTpooled	1.19017	0.362
IL12-4/WTpooled	1.4369	0.673
IL1-4/WTpooled	0.76944
WT/WTpooled	0.9772	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01151	1
DC3000/delta hrp 6h	0.56567	0.485
DC3000/delta hrp 12h	1.02247	1
DC3000/delta hrp 24h	2.07576	0.03

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	0.68975	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02614	1
Var 0h	0.87632	1
Var 12h I row2-row1	1.38926	0.654
Var 12h NI row2-row1	1.35344	0.649
Var 36h I row2-row1	1.06144	0.742
Var 36h NI row2-row1	0.67715	0.347
Var 60h I row2-row1	0.84498	0.292
Var 60h NI row2-row1	0.87051	0.977
Time course 0hI-0hNI	0.93738	0.618
Time course 12hI-12hNI	0.88828	0.177
Time course 36hI-36hNI	0.72004	0.046
Time course 60hI-60hNI	1.59123	0.01

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)	1.46325	0.326
transgenic ySAMdc/azygous control (breaker)	0.51722	0.131
transgenic ySAMdc/azygous control (red)	0.65345	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03016	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.45499	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.28607	0.14
Manapal/WT (break)	1.46409	1
Manapal/WT (red)	1.4457	0.413