Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.9.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28399	0.463
27DAP/17DAP	0.78289	0.373
39DAP/27DAP	1.51627	0.128
41DAP/39DAP	1.18619	0.806
42DAP/41DAP	0.94091	1
43DAP/42DAP	1.02743	1
47DAP/43DAP	1.09067	0.793
52DAP/47DAP	1.24219	0.651
57DAP/52DAP	0.95913	0.956

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69751	0.012
17DAP/reference	1.18842	0.412
27DAP/reference	0.81724	0.07
39DAP/reference	1.19559	0.497
41DAP/reference	1.18976	0.203
42DAP/reference	1.45383	0.002
43DAP/reference	1.30486	0.025
47DAP/reference	1.15661	0.404
52DAP/reference	0.91403	0.25
57DAP/reference	1.19189	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94524	0.56
27DAP/17DAP	1.00669	1
39DAP/27DAP	1.0299	0.77
41DAP/39DAP	1.03795	0.781
42DAP/41DAP	1.04706	0.81
43DAP/42DAP	1.07297	0.056
47DAP/43DAP	1.05318	0.749
52DAP/47DAP	0.88003	0.405
57DAP/52DAP	0.91702	0.428
57DAP/7DAP	0.98792	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73394	0.024
17DAP/reference	1.52681	0.008
27DAP/reference	1.61138	0.007
39DAP/reference	1.45046	0.005
41DAP/reference	1.44383	0.017
42DAP/reference	1.24491	0.174
43DAP/reference	1.27191	0.015
47DAP/reference	1.44593	0.023
52DAP/reference	1.93883	0.026
57DAP/reference	2.12392	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26468	0.175
17DAP/reference	1.7291	0.007
27DAP/reference	1.50658	0.014
39DAP/reference	1.34706	0.013
41DAP/reference	1.59786	0.006
42DAP/reference	1.70048	0.007
43DAP/reference	1.46202	0.117
47DAP/reference	1.99387	0.008
52DAP/reference	1.11623	0.085
57DAP/reference	1.207	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39061	0.015
17DAP/reference	1.17769	0.143
27DAP/reference	1.14733	0.067
39DAP/reference	1.467	0.005
41DAP/reference	1.31953	0.011
42DAP/reference	1.36194	0.013
43DAP/reference	1.60037	0.02
47DAP/reference	1.13287	0.12
52DAP/reference	1.48635	0.048
57DAP/reference	1.19381	0.218

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10999	1
26DAP/20DAP	0.92074	1
34DAP/26DAP	1.0136	1
51DAP/34DAP	0.92313	0.546
52DAP/51DAP	0.91992	1
53DAP/52DAP	1.05913	0.783
55DAP/53DAP	1.00731	0.964
57DAP/55DAP	1.11761	0.841
62DAP/57DAP	1.39239	0.257
68DAP/62DAP	0.87059	0.641
68DAP/14DAP	0.86021	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.4859	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82376	0.279
Mature Green Tomato/Ripe Tomato	1.2023	0.437
Immature Eggplant/Mature Eggplant	1.13536	0.334
Ripe Pepper/Ripe Tomato	1.46035	0.258
Mature Eggplant/Ripe Tomato	2.12314

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.17567
12-2/M82	N/A	N/A
12-4/M82	1.13731
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.27829
4-3-2/M82	1.48697
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	N/A	N/A
9-3-2/M82	0.88057	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08559	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13042	1
IL12-4/WTpooled	1.12233	0.52
IL1-4/WTpooled	1.21016	1
WT/WTpooled	1.08525	0.957

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	1.00666	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.19622	0.921
DC3000/delta hrp 6h	0.96169	0.95
DC3000/delta hrp 12h	0.90286	1
DC3000/delta hrp 24h	1.50381	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.14874	0.16
DC3000 delta B/DC3000 delta AB	0.88113	0.288

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84021	1
Exp 36h	1.16117	1
Exp 60h	1.04617	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9652	1
Var 0h	0.74954	0.98
Var 12h I row2-row1	0.88092	0.514
Var 12h NI row2-row1	0.88957	0.627
Var 36h I row2-row1	1.03187	1
Var 36h NI row2-row1	1.02754	1
Var 60h I row2-row1	1.00565	1
Var 60h NI row2-row1	0.87784	0.458
Time course 0hI-0hNI	0.95968	0.729
Time course 12hI-12hNI	1.00744	0.861
Time course 36hI-36hNI	0.95878	0.344
Time course 60hI-60hNI	1.09861	0.16

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)	0.97406	0.33
transgenic ySAMdc/azygous control (breaker)	1.16694	1
transgenic ySAMdc/azygous control (red)	1.26412	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22873	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.805	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.54817	0.172
Manapal/WT (break)	0.83266	0.333
Manapal/WT (red)	1.28241	0.413