Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.16.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95769	0.728
27DAP/17DAP	1.08571	0.905
39DAP/27DAP	0.79297	0.402
41DAP/39DAP	1.13047	0.638
42DAP/41DAP	0.9362	1
43DAP/42DAP	1.0249	1
47DAP/43DAP	0.84194	0.504
52DAP/47DAP	0.72932	0.37
57DAP/52DAP	1.09203	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93626	0.217
17DAP/reference	1.04119	0.178
27DAP/reference	1.02055	0.759
39DAP/reference	1.06755	0.157
41DAP/reference	1.0191	0.963
42DAP/reference	0.93705	0.048
43DAP/reference	1.02339	0.705
47DAP/reference	1.04786	0.379
52DAP/reference	1.00235	1
57DAP/reference	0.98502	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94104	0.56
27DAP/17DAP	1.15755	0.771
39DAP/27DAP	1.23507	0.394
41DAP/39DAP	1.11588	0.883
42DAP/41DAP	1.02834	0.924
43DAP/42DAP	1.08636	0.788
47DAP/43DAP	0.90558	0.339
52DAP/47DAP	1.30538	0.412
57DAP/52DAP	0.95343	0.651
57DAP/7DAP	1.6434	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96462	0.246
17DAP/reference	1.00043	1
27DAP/reference	0.93853	0.066
39DAP/reference	0.98504	0.354
41DAP/reference	0.98238	0.16
42DAP/reference	0.9603	0.05
43DAP/reference	0.95674	0.072
47DAP/reference	0.96072	0.383
52DAP/reference	0.91219	0.053
57DAP/reference	0.95073	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90926	0.037
17DAP/reference	0.88252	0.014
27DAP/reference	0.849	0.1
39DAP/reference	0.8319	0.083
41DAP/reference	0.97119	0.493
42DAP/reference	0.95832	0.289
43DAP/reference	0.85471	0.027
47DAP/reference	0.96771	0.349
52DAP/reference	0.94173	0.143
57DAP/reference	0.97238	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89118	0.074
17DAP/reference	0.93516	0.292
27DAP/reference	0.97691	0.397
39DAP/reference	0.96476	0.163
41DAP/reference	1.00663	0.984
42DAP/reference	0.89568	0.036
43DAP/reference	0.9702	0.468
47DAP/reference	0.92471	0.207
52DAP/reference	0.95422	0.482
57DAP/reference	0.93568	0.238

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00749	1
26DAP/20DAP	0.72265	0.317
34DAP/26DAP	1.02857	1
51DAP/34DAP	1.03961	0.799
52DAP/51DAP	1.13789	0.836
53DAP/52DAP	1.11511	0.819
55DAP/53DAP	1.1752	0.511
57DAP/55DAP	0.83036	0.294
62DAP/57DAP	1.02836	1
68DAP/62DAP	1.01766	1
68DAP/14DAP	1.05207	0.656

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72713	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79112	0.268
Mature Green Tomato/Ripe Tomato	1.10418	0.715
Immature Eggplant/Mature Eggplant	0.95911	0.651
Ripe Pepper/Ripe Tomato	1.86048	0.258
Mature Eggplant/Ripe Tomato	1.84598

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.896
1-1-2/M82	0.89904	1
12-2/M82	N/A	N/A
12-4/M82	0.77063	0.619
1-3/M82	N/A	N/A
2-1-1/M82	0.71415
2-1/M82	N/A	N/A
2-6/M82	0.78984
3-2/M82	1.3638	0.84
4-1-1/M82	N/A	N/A
4-1/M82	0.59359
4-3-2/M82	0.95428	1
4-3/M82	1.08921
5-3/M82	1.04791	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	1.1901
9-3-2/M82	0.85512	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.04652	1
IL2-6/WTpooled	1.04241	1
IL7-5/WTpooled	0.94289	1
IL7-3/WTpooled	1.12755	0.362
IL12-4/WTpooled	1.64684	0.546
IL1-4/WTpooled	0.94055	0.834
WT/WTpooled	0.911	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	1.07456	0.921
DC3000/delta hrp 6h	0.98405	0.95
DC3000/delta hrp 12h	1.02154	1
DC3000/delta hrp 24h	1.07013	0.397

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	0.74059	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11017	0.254
Exp 36h	1.4485	0.693
Exp 60h	1.46408	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.92247	1
Var 0h	1.34936	0.98
Var 12h I row2-row1	1.56944	0.473
Var 12h NI row2-row1	1.17951	1
Var 36h I row2-row1	1.0383	1
Var 36h NI row2-row1	0.84869	0.225
Var 60h I row2-row1	1.10487	0.523
Var 60h NI row2-row1	0.96124	1
Time course 0hI-0hNI	1.02118	1
Time course 12hI-12hNI	0.82924	0.212
Time course 36hI-36hNI	0.92269	0.22
Time course 60hI-60hNI	1.3467	0.012

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)	1.02587	0.699
transgenic ySAMdc/azygous control (breaker)	1.40216	0.178
transgenic ySAMdc/azygous control (red)	1.02621	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97715	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87157	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83444	0.172
Manapal/WT (break)	0.7829	0.299
Manapal/WT (red)	0.88445	0.607