Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19512	0.798
27DAP/17DAP	1.04742	0.992
39DAP/27DAP	1.11169	0.981
41DAP/39DAP	0.9705	0.879
42DAP/41DAP	0.97199	1
43DAP/42DAP	0.90522	0.829
47DAP/43DAP	1.45136	0.229
52DAP/47DAP	1.03034	0.816
57DAP/52DAP	0.86511	0.845

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81134	0.028
17DAP/reference	0.95143	0.321
27DAP/reference	1.05171	0.794
39DAP/reference	0.94176	0.412
41DAP/reference	0.90006	0.341
42DAP/reference	0.84995	0.002
43DAP/reference	0.92401	0.302
47DAP/reference	0.95805	0.279
52DAP/reference	1.1052	0.453
57DAP/reference	1.05147	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47883	0.061
27DAP/17DAP	0.85563	0.648
39DAP/27DAP	1.01731	1
41DAP/39DAP	0.83215	0.299
42DAP/41DAP	1.13135	0.081
43DAP/42DAP	1.14739	0.297
47DAP/43DAP	1.00736	1
52DAP/47DAP	0.91367	0.702
57DAP/52DAP	1.08713	0.732
57DAP/7DAP	1.13002	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31244	0.07
17DAP/reference	1.08976	0.399
27DAP/reference	0.89076	0.101
39DAP/reference	1.85678	0.705
41DAP/reference	0.92968	0.326
42DAP/reference	0.75035	0.063
43DAP/reference	0.95125	0.334
47DAP/reference	0.99765	1
52DAP/reference	1.04695	0.732
57DAP/reference	1.07224	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78005	0.04
17DAP/reference	0.63635	0.003
27DAP/reference	0.76625	0.026
39DAP/reference	0.87799	0.045
41DAP/reference	0.89673	0.177
42DAP/reference	0.77725	0.027
43DAP/reference	0.74767	0.039
47DAP/reference	0.91949	0.201
52DAP/reference	0.87045	0.04
57DAP/reference	0.76785	0.021

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9783	0.566
17DAP/reference	0.90956	0.313
27DAP/reference	0.93366	0.14
39DAP/reference	0.94847	0.222
41DAP/reference	0.9951	0.754
42DAP/reference	0.887	0.22
43DAP/reference	0.91569	0.059
47DAP/reference	0.98658	0.574
52DAP/reference	0.75451	0.098
57DAP/reference	1.04481	0.878

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05922	0.966
26DAP/20DAP	1.11019	0.798
34DAP/26DAP	0.89647	0.619
51DAP/34DAP	1.62848	0.032
52DAP/51DAP	0.90596	1
53DAP/52DAP	1.3274	0.108
55DAP/53DAP	0.95317	0.775
57DAP/55DAP	1.06218	0.968
62DAP/57DAP	1.13253	0.723
68DAP/62DAP	1.09008	1
68DAP/14DAP	1.70551	0.022

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.09462	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.69812	0.212
Mature Green Tomato/Ripe Tomato	0.67525	0.026
Immature Eggplant/Mature Eggplant	0.95878	0.134
Ripe Pepper/Ripe Tomato	0.79942	0.293
Mature Eggplant/Ripe Tomato	0.90392	1

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	0.67405
1-3/M82	1.86966
2-1-1/M82	0.87224
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.81218	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.98509
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.92905	1
IL2-6/WTpooled	0.88127	1
IL7-5/WTpooled	1.17848	0.792
IL7-3/WTpooled	1.01827	1
IL12-4/WTpooled	1.14403	0.538
IL1-4/WTpooled	0.94509	0.457
WT/WTpooled	1.03496	0.911

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	0.84032	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02457	0.921
DC3000/delta hrp 6h	1.07947	1
DC3000/delta hrp 12h	1.00698	1
DC3000/delta hrp 24h	0.97923	0.945

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	1.33468

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.10341	1
Exp 60h	0.7511	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	0.80723
Var 0h	N/A	N/A
Var 12h I row2-row1	1.47396	0.324
Var 12h NI row2-row1	0.9048	0.713
Var 36h I row2-row1	1.74511	0.908
Var 36h NI row2-row1	1.0099
Var 60h I row2-row1	1.10813	1
Var 60h NI row2-row1	1.31813	0.362
Time course 0hI-0hNI	1.21701	0.719
Time course 12hI-12hNI	1.30779	0.265
Time course 36hI-36hNI	1.08201	1
Time course 60hI-60hNI	0.95338	0.646

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)	0.96958	0.614
transgenic ySAMdc/azygous control (breaker)	0.94	0.49
transgenic ySAMdc/azygous control (red)	0.89026	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.24479	0.034

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00594	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03118	1
Manapal/WT (break)	1.57349	0.381
Manapal/WT (red)	2.1033	0.137