Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73557	0.211
27DAP/17DAP	0.86984	0.561
39DAP/27DAP	1.80596	0.189
41DAP/39DAP	1.00902	0.89
42DAP/41DAP	1.01753	1
43DAP/42DAP	1.10152	1
47DAP/43DAP	0.64665	0.148
52DAP/47DAP	1.2229	0.946
57DAP/52DAP	1.26688	0.964

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.25526	0.081
17DAP/reference	0.61792	0.018
27DAP/reference	0.80329	0.011
39DAP/reference	0.77476	0.009
41DAP/reference	0.65157	0.009
42DAP/reference	1.07825	0.842
43DAP/reference	1.01059
47DAP/reference	1.41253	0.012
52DAP/reference	1.6695	0.022
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.48617	0.047
27DAP/17DAP	1.20857	0.377
39DAP/27DAP	0.82617	0.215
41DAP/39DAP	1.19332	0.997
42DAP/41DAP	1.26095	0.495
43DAP/42DAP	0.77209	0.043
47DAP/43DAP	1.03037	0.973
52DAP/47DAP	1.04851	0.973
57DAP/52DAP	1.23904	0.197
57DAP/7DAP	1.2831	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47254	0.041
17DAP/reference	1.1695	0.035
27DAP/reference	1.3118	0.023
39DAP/reference	1.48826	0.006
41DAP/reference	1.27405	0.042
42DAP/reference	1.59706	0.016
43DAP/reference	1.52389	0.01
47DAP/reference	2.0954	0.019
52DAP/reference	1.52088	0.017
57DAP/reference	1.24524	0.037

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01988	0.848
17DAP/reference	0.90687	0.269
27DAP/reference	1.43564	0.249
39DAP/reference	1.22605	0.571
41DAP/reference	1.16753	0.372
42DAP/reference	1.41559	0.086
43DAP/reference	1.02723	0.706
47DAP/reference	1.17891	0.388
52DAP/reference	0.71757	0.004
57DAP/reference	0.64316	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44937	0.03
17DAP/reference	0.93521	0.477
27DAP/reference	1.23132	0.065
39DAP/reference	1.57876	0.019
41DAP/reference	1.21353	0.069
42DAP/reference	1.62566	0.012
43DAP/reference	1.47172	0.05
47DAP/reference	0.97649	0.465
52DAP/reference	1.47816	0.063
57DAP/reference	3.64676	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07489	0.966
26DAP/20DAP	1.70152	0.133
34DAP/26DAP	0.79336	0.165
51DAP/34DAP	3.32953	0.029
52DAP/51DAP	0.87063	1
53DAP/52DAP	1.62171	0.057
55DAP/53DAP	0.74048	0.125
57DAP/55DAP	0.76581	0.178
62DAP/57DAP	0.83613	0.681
68DAP/62DAP	1.13341	0.858
68DAP/14DAP	2.56953	0.067

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75251	0.049

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74724	0.213
Mature Green Tomato/Ripe Tomato	1.09575	0.69
Immature Eggplant/Mature Eggplant	2.16571	0.05
Ripe Pepper/Ripe Tomato	1.33185	0.256
Mature Eggplant/Ripe Tomato	0.623	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.09454	1
12-2/M82	0.96844	1
12-4/M82	1.11127	1
1-3/M82	3.15476
2-1-1/M82	0.89542
2-1/M82	0.56137
2-6/M82	0.66427	0.501
3-2/M82	1.01561
4-1-1/M82	0.67499	1
4-1/M82	1.42054	1
4-3-2/M82	0.9916	1
4-3/M82	1.08288	1
5-3/M82	1.16516	1
6-2/M82	0.81178
6-3/M82	0.83314	1
7-1/M82	0.74004	0.476
7-2/M82	1.07605
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.75264
IL12-4/WTpooled	1.05382	0.891
IL1-4/WTpooled	0.96106	0.341
WT/WTpooled	1.24111	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	1.06396	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.27629	0.724
DC3000/delta hrp 6h	0.91739	0.95
DC3000/delta hrp 12h	0.96775	1
DC3000/delta hrp 24h	0.8487	0.143

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.29716	0.042
DC3000 delta B/DC3000 delta AB	1.35007	0.112

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.24736	1
Exp 36h	1.30465	1
Exp 60h	1.44444	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99123	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.81197
Var 12h NI row2-row1	0.95945
Var 36h I row2-row1	1.16862	0.291
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.96629	0.866
Time course 12hI-12hNI	1.13717	0.603
Time course 36hI-36hNI	1.37186	0.021
Time course 60hI-60hNI	1.98851	0.008

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)	0.81658	0.324
transgenic ySAMdc/azygous control (breaker)	0.64494	0.173
transgenic ySAMdc/azygous control (red)	1.01665	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22718	0.073

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.79479	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06004	1
Manapal/WT (break)	1.40499	0.183
Manapal/WT (red)	0.86708	0.181