Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84781	0.052
27DAP/17DAP	0.98282	0.945
39DAP/27DAP	1.2631	0.699
41DAP/39DAP	0.57076	0.045
42DAP/41DAP	0.83033	1
43DAP/42DAP	1.11111	1
47DAP/43DAP	0.34288	0.049
52DAP/47DAP	0.8998	0.702
57DAP/52DAP	0.89881	0.729

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01575	0.844
17DAP/reference	1.19983	0.318
27DAP/reference	0.97893	0.694
39DAP/reference	1.01186	0.885
41DAP/reference	0.89487	0.341
42DAP/reference	0.71413	0.001
43DAP/reference	0.72778	0.118
47DAP/reference	0.57078	0.001
52DAP/reference	0.54572	0.042
57DAP/reference	0.91199	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.28677	0.036
27DAP/17DAP	0.77306	0.187
39DAP/27DAP	0.72023	0.1
41DAP/39DAP	1.02059	0.968
42DAP/41DAP	0.88148	0.365
43DAP/42DAP	1.17406	0.112
47DAP/43DAP	0.7437	0.055
52DAP/47DAP	1.25348	0.354
57DAP/52DAP	1.02892	0.895
57DAP/7DAP	0.92927	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.19992	0.024
17DAP/reference	1.49871	0.007
27DAP/reference	0.93543	0.055
39DAP/reference	1.80755	0.014
41DAP/reference	0.94587	0.357
42DAP/reference	1.12941	0.686
43DAP/reference	0.95425	0.385
47DAP/reference	0.97166	0.671
52DAP/reference	0.80505	0.043
57DAP/reference	0.84895	0.052

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85892	0.17
17DAP/reference	1.04345	0.924
27DAP/reference	1.06662	1
39DAP/reference	1.15172	0.146
41DAP/reference	1.0836	0.491
42DAP/reference	0.99877	0.723
43DAP/reference	0.69988	0.034
47DAP/reference	1.13047	0.089
52DAP/reference	1.02875	0.938
57DAP/reference	0.63358	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.50103	0.015
17DAP/reference	2.63921	0.075
27DAP/reference	2.13979	0.016
39DAP/reference	2.29985	0.006
41DAP/reference	1.43073	0.022
42DAP/reference	0.93319	0.361
43DAP/reference	0.86169	0.216
47DAP/reference	0.62239	0.005
52DAP/reference	0.74883	0.172
57DAP/reference	1.16938	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13745	0.966
26DAP/20DAP	1.56364	0.101
34DAP/26DAP	1.12773	0.819
51DAP/34DAP	0.99987	0.927
52DAP/51DAP	1.24859	0.073
53DAP/52DAP	0.80888	0.133
55DAP/53DAP	0.98847	0.894
57DAP/55DAP	0.97745	0.854
62DAP/57DAP	0.72166	0.05
68DAP/62DAP	1.07994	0.926
68DAP/14DAP	0.83602	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30765	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.56137	0.058
Mature Green Tomato/Ripe Tomato	14.6825	0.015
Immature Eggplant/Mature Eggplant	0.23896	0.057
Ripe Pepper/Ripe Tomato	2.0254	0.256
Mature Eggplant/Ripe Tomato	5.77558	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93892	0.944
1-1-2/M82	N/A	N/A
12-2/M82	1.46876
12-4/M82	1.77046	1
1-3/M82	0.78508
2-1-1/M82	1.02685	1
2-1/M82	N/A	N/A
2-6/M82	1.02193	0.594
3-2/M82	N/A	N/A
4-1-1/M82	1.23916	0.876
4-1/M82	1.29893
4-3-2/M82	N/A	N/A
4-3/M82	1.13017
5-3/M82	1.06203	1
6-2/M82	1.27778	0.253
6-3/M82	1.05703	1
7-1/M82	N/A	N/A
7-2/M82	1.28747	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.48398	0.277
IL2-6/WTpooled	0.53153	0.337
IL7-5/WTpooled	0.95408	1
IL7-3/WTpooled	1.29128	1
IL12-4/WTpooled	0.94655	1
IL1-4/WTpooled	0.93193	0.834
WT/WTpooled	1.03343	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	1.23604	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9791	1
DC3000/delta hrp 6h	0.90818	0.95
DC3000/delta hrp 12h	1.59685
DC3000/delta hrp 24h	0.89785	0.207

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53934	0.043
DC3000 delta B/DC3000 delta AB	0.49726	0.02

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99396	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.8638	0.357
Var 12h NI row2-row1	0.99384	1
Var 36h I row2-row1	0.9607	0.805
Var 36h NI row2-row1	1.3904	1
Var 60h I row2-row1	1.23877	0.562
Var 60h NI row2-row1	0.88779	0.932
Time course 0hI-0hNI	0.97552	0.881
Time course 12hI-12hNI	1.00763	0.9
Time course 36hI-36hNI	0.98321	0.589
Time course 60hI-60hNI	0.50768	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)	1.0358	0.798
transgenic ySAMdc/azygous control (breaker)	1.04868	1
transgenic ySAMdc/azygous control (red)	1.63368	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.80996	0.126

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.55011	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.36264	0.307
Manapal/WT (break)	1.35745	0.183
Manapal/WT (red)	2.70926	0.137