Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.1.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15911	0.512
27DAP/17DAP	1.07513	1
39DAP/27DAP	0.70962	0.069
41DAP/39DAP	1.2257	0.437
42DAP/41DAP	0.85456	1
43DAP/42DAP	1.02765	1
47DAP/43DAP	1.37815	0.172
52DAP/47DAP	0.94718	0.786
57DAP/52DAP	0.86403	0.824

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83654	0.39
17DAP/reference	0.82585	0.208
27DAP/reference	1.24832	0.014
39DAP/reference	1.09043	1
41DAP/reference	0.80776	0.434
42DAP/reference	1.25127	0.264
43DAP/reference	0.86462	0.346
47DAP/reference	1.1638	0.11
52DAP/reference	0.97438	0.546
57DAP/reference	1.21093	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9124	0.323
27DAP/17DAP	1.03988	0.968
39DAP/27DAP	0.99068	0.953
41DAP/39DAP	1.12783	0.887
42DAP/41DAP	1.00416	0.92
43DAP/42DAP	1.05349	0.351
47DAP/43DAP	0.96711	0.87
52DAP/47DAP	1.44919	0.317
57DAP/52DAP	0.99004	0.818
57DAP/7DAP	2.86804	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8808	0.183
17DAP/reference	0.89726	0.082
27DAP/reference	1.05143	0.804
39DAP/reference	0.77777	0.011
41DAP/reference	0.72976	0.044
42DAP/reference	0.67218	0.013
43DAP/reference	0.78973	0.023
47DAP/reference	0.77281	0.222
52DAP/reference	0.73506	0.024
57DAP/reference	0.85389	0.077

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89142	0.399
17DAP/reference	1.29592	0.789
27DAP/reference	1.03003	0.686
39DAP/reference	1.21334	0.424
41DAP/reference	1.20679	1
42DAP/reference	1.21193	0.153
43DAP/reference	1.49058	0.185
47DAP/reference	1.20705	0.695
52DAP/reference	1.29237	0.3
57DAP/reference	1.23253	0.626

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85886	0.098
17DAP/reference	0.94112	0.477
27DAP/reference	0.75162	0.026
39DAP/reference	0.80934	0.011
41DAP/reference	0.91077	0.086
42DAP/reference	1.06534	0.893
43DAP/reference	0.80796	0.031
47DAP/reference	1.06692	1
52DAP/reference	2.14087	0.161
57DAP/reference	1.26849	0.604

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.57059
26DAP/20DAP	0.78959	0.512
34DAP/26DAP	1.22996	0.819
51DAP/34DAP	1.2151	0.064
52DAP/51DAP	1.09063	0.776
53DAP/52DAP	1.00022	0.97
55DAP/53DAP	1.10548	0.764
57DAP/55DAP	0.92614	0.658
62DAP/57DAP	1.00742	0.994
68DAP/62DAP	0.86853	0.032
68DAP/14DAP	1.03221

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.32401	0.369

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.44129	0.363
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.77166
Mature Eggplant/Ripe Tomato	0.74168

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91964	0.944
1-1-2/M82	1.07349	1
12-2/M82	1.09724	0.61
12-4/M82	0.96417	1
1-3/M82	0.93536	1
2-1-1/M82	1.095
2-1/M82	0.87594	0.74
2-6/M82	1.08827	1
3-2/M82	0.87713
4-1-1/M82	1.02969	1
4-1/M82	0.88439	1
4-3-2/M82	1.05279	1
4-3/M82	0.94152	1
5-3/M82	1.02138	1
6-2/M82	0.81373	1
6-3/M82	1.10466	1
7-1/M82	0.89869	0.509
7-2/M82	1.00455	1
9-3-2/M82	0.79368	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.02371	1
IL2-6/WTpooled	1.01595	1
IL7-5/WTpooled	0.98928
IL7-3/WTpooled	1.05621	1
IL12-4/WTpooled	1.14098	0.673
IL1-4/WTpooled	0.87396	0.699
WT/WTpooled	1.13204	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	0.84417	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.24302	0.921
DC3000/delta hrp 6h	0.49106
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.90105	0.292

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97047	0.841
DC3000 delta B/DC3000 delta AB	0.96524	0.745

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09117	1
Exp 36h	N/A	N/A
Exp 60h	1.08027	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96738	1
Var 0h	1.02479	1
Var 12h I row2-row1	0.96973	0.948
Var 12h NI row2-row1	0.82408	0.546
Var 36h I row2-row1	0.84525	0.805
Var 36h NI row2-row1	1.3666	0.482
Var 60h I row2-row1	1.05382	0.562
Var 60h NI row2-row1	1.1886	0.904
Time course 0hI-0hNI	0.98109	0.945
Time course 12hI-12hNI	1.05559	0.861
Time course 36hI-36hNI	0.84155	0.096
Time course 60hI-60hNI	0.55523	0.006

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)	1.16841	0.212
transgenic ySAMdc/azygous control (breaker)	0.81095	0.173
transgenic ySAMdc/azygous control (red)	0.85125	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8074	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.08844	1
Manapal/WT (red)	1.07098	0.413