Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.47815	0.019
27DAP/17DAP	0.51494	0.041
39DAP/27DAP	1.09681	0.769
41DAP/39DAP	0.78507	0.407
42DAP/41DAP	0.99457	1
43DAP/42DAP	1.3578	0.655
47DAP/43DAP	1.03639	0.902
52DAP/47DAP	0.9209	0.821
57DAP/52DAP	1.24976	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33396	0.041
17DAP/reference	1.12365	0.546
27DAP/reference	1.18365	0.252
39DAP/reference	1.15069	0.174
41DAP/reference	1.40358	0.019
42DAP/reference	1.10133	0.485
43DAP/reference	1.08835	0.73
47DAP/reference	1.16994	0.72
52DAP/reference	1.21182	0.302
57DAP/reference	1.24248	0.419

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.3848	0.024
27DAP/17DAP	1.29806	0.178
39DAP/27DAP	0.50284	0.035
41DAP/39DAP	0.77224	0.158
42DAP/41DAP	1.02295	0.835
43DAP/42DAP	1.15288	0.478
47DAP/43DAP	0.80199	0.051
52DAP/47DAP	0.95663	0.839
57DAP/52DAP	1.08904	0.899
57DAP/7DAP	0.23375	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.82983	0.034
17DAP/reference	1.22529	0.199
27DAP/reference	0.9781	0.494
39DAP/reference	0.54511	0.011
41DAP/reference	0.72895	0.02
42DAP/reference	0.63617	0.015
43DAP/reference	0.68373	0.011
47DAP/reference	0.84026	0.293
52DAP/reference	0.65277	0.012
57DAP/reference	0.62927	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93061	0.592
17DAP/reference	1.2267	0.11
27DAP/reference	1.13615	0.48
39DAP/reference	1.12304	0.848
41DAP/reference	1.00777	0.683
42DAP/reference	0.85954	0.355
43DAP/reference	0.98823	0.633
47DAP/reference	1.24963	0.026
52DAP/reference	0.99863	0.666
57DAP/reference	1.10046	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.67078	0.015
17DAP/reference	1.39543	0.168
27DAP/reference	1.13425	0.408
39DAP/reference	0.99525	0.755
41DAP/reference	0.93639	0.459
42DAP/reference	0.90076	0.361
43DAP/reference	0.78267	0.106
47DAP/reference	1.07811	0.73
52DAP/reference	1.26571	0.928
57DAP/reference	0.70716	0.105

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.67783
26DAP/20DAP	1.18445	0.598
34DAP/26DAP	1.15366	1
51DAP/34DAP	0.55084	0.054
52DAP/51DAP	0.81133	1
53DAP/52DAP	1.05016	0.819
55DAP/53DAP	0.84586	0.091
57DAP/55DAP	1.07645	0.909
62DAP/57DAP	0.70262	0.162
68DAP/62DAP	1.15467	0.939
68DAP/14DAP	0.95211	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.12421	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.8598
Mature Green Tomato/Ripe Tomato	6.25079	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	10.6768
Mature Eggplant/Ripe Tomato	2.5267	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.74967
12-2/M82	0.74461
12-4/M82	1.09941	1
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	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.06187
6-2/M82	N/A	N/A
6-3/M82	0.64069
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	0.80171	0.243
IL2-6/WTpooled	0.97579	1
IL7-5/WTpooled	0.95274	0.31
IL7-3/WTpooled	0.85256	0.418
IL12-4/WTpooled	0.97294	1
IL1-4/WTpooled	0.89934	0.699
WT/WTpooled	0.99855	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	0.96875	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0056	1
DC3000/delta hrp 6h	0.97904
DC3000/delta hrp 12h	1.42029	1
DC3000/delta hrp 24h	0.41025	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.29078	0.023
DC3000 delta B/DC3000 delta AB	0.36978	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.25992	1
Exp 36h	0.64194	0.589
Exp 60h	0.82254	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01338	1
Var 0h	0.14448	1
Var 12h I row2-row1	0.74617	0.338
Var 12h NI row2-row1	0.88643	0.713
Var 36h I row2-row1	0.87719	0.575
Var 36h NI row2-row1	0.8948	1
Var 60h I row2-row1	0.8083	0.285
Var 60h NI row2-row1	1.23625	0.904
Time course 0hI-0hNI	1.00541	1
Time course 12hI-12hNI	0.82925	0.132
Time course 36hI-36hNI	0.73247	0.029
Time course 60hI-60hNI	0.20435	0.005

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)	1.01424	1
transgenic ySAMdc/azygous control (breaker)	0.81707	0.49
transgenic ySAMdc/azygous control (red)	0.9481	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.13856	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.49236	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03411	1
Manapal/WT (break)	0.94801	1
Manapal/WT (red)	1.32942	1