Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.1.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.72569	0.13
27DAP/17DAP	1.11047	0.849
39DAP/27DAP	0.83036	0.447
41DAP/39DAP	1.02532	0.935
42DAP/41DAP	1.24018	0.844
43DAP/42DAP	1.02514	0.937
47DAP/43DAP	0.98914	0.84
52DAP/47DAP	0.75704	0.425
57DAP/52DAP	1.08837	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63702	0.024
17DAP/reference	1.22879	0.154
27DAP/reference	1.5871	0.01
39DAP/reference	1.51411	0.014
41DAP/reference	1.14518	0.203
42DAP/reference	1.57731	0.001
43DAP/reference	1.8305	0.007
47DAP/reference	3.19799	0.001
52DAP/reference	3.6255	0.007
57DAP/reference	2.54477	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7448	0.096
27DAP/17DAP	1.33315	0.069
39DAP/27DAP	0.90852	0.432
41DAP/39DAP	0.84414	0.087
42DAP/41DAP	0.91116	0.243
43DAP/42DAP	1.03267	0.699
47DAP/43DAP	1.06763	0.827
52DAP/47DAP	1.49373	0.121
57DAP/52DAP	1.51201	0.082
57DAP/7DAP	1.08967	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76276	0.066
17DAP/reference	0.99134	0.599
27DAP/reference	0.90979	0.016
39DAP/reference	1.60129	0.005
41DAP/reference	0.94293	0.271
42DAP/reference	1.39955	0.018
43DAP/reference	1.47961	0.02
47DAP/reference	1.67119	0.033
52DAP/reference	1.49475	0.052
57DAP/reference	1.8139	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68405	0.017
17DAP/reference	1.44275	0.01
27DAP/reference	1.16907	0.352
39DAP/reference	1.75555	0.011
41DAP/reference	1.47065	0.038
42DAP/reference	1.41387	0.011
43DAP/reference	1.1079	0.835
47DAP/reference	1.8702	0.008
52DAP/reference	1.1456	0.168
57DAP/reference	1.11287	0.552

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.53684	0.028
17DAP/reference	0.65374	0.011
27DAP/reference	0.72187	0.025
39DAP/reference	0.85396	0.069
41DAP/reference	0.8876	0.064
42DAP/reference	1.41154	0.018
43DAP/reference	1.74135	0.01
47DAP/reference	2.43551	0.005
52DAP/reference	2.25441	0.028
57DAP/reference	6.59655	0.004

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10417	0.966
26DAP/20DAP	1.02145	1
34DAP/26DAP	1.00356	1
51DAP/34DAP	0.83036	0.155
52DAP/51DAP	1.21517	0.232
53DAP/52DAP	0.94026	0.79
55DAP/53DAP	1.214	0.185
57DAP/55DAP	0.64024	0.035
62DAP/57DAP	0.72558	0.028
68DAP/62DAP	1.15612	0.549
68DAP/14DAP	1.33146	0.189

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.88717	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15427	0.089
Mature Green Tomato/Ripe Tomato	0.98176	0.774
Immature Eggplant/Mature Eggplant	0.97938	0.72
Ripe Pepper/Ripe Tomato	0.11035	0.224
Mature Eggplant/Ripe Tomato	0.16473	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37421	0.742
1-1-2/M82	1.24519	0.891
12-2/M82	1.15878	1
12-4/M82	0.99068	1
1-3/M82	1.99106	0.255
2-1-1/M82	1.05759	1
2-1/M82	0.74908	0.322
2-6/M82	1.23705	0.594
3-2/M82	0.843
4-1-1/M82	0.94045	1
4-1/M82	1.04709	1
4-3-2/M82	1.31749
4-3/M82	1.15699	1
5-3/M82	0.82186	0.447
6-2/M82	0.84296	1
6-3/M82	0.97326	1
7-1/M82	0.9772	1
7-2/M82	1.06336	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97332	1
IL2-6/WTpooled	0.65113
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.90115
IL12-4/WTpooled	0.83634	0.71
IL1-4/WTpooled	1.40187	0.395
WT/WTpooled	0.88436	0.881

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	1.10345	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08468	0.875
DC3000/delta hrp 6h	0.99069	0.95
DC3000/delta hrp 12h	1.35295	1
DC3000/delta hrp 24h	0.77309	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17784	0.29
DC3000 delta B/DC3000 delta AB	1.06143	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08145	1
Exp 36h	0.75653	0.434
Exp 60h	0.8697	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01107	1
Var 0h	1.02632	1
Var 12h I row2-row1	1.00543	1
Var 12h NI row2-row1	1.19935	0.649
Var 36h I row2-row1	1.02883	1
Var 36h NI row2-row1	0.93652	0.791
Var 60h I row2-row1	1.02763	1
Var 60h NI row2-row1	0.81608	0.431
Time course 0hI-0hNI	0.96508	0.751
Time course 12hI-12hNI	0.95244	0.47
Time course 36hI-36hNI	1.0358	0.58
Time course 60hI-60hNI	0.81472	0.009

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)	1.1309	0.384
transgenic ySAMdc/azygous control (breaker)	0.6588	0.125
transgenic ySAMdc/azygous control (red)	1.0274	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.22069	0.13

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.62605	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.52299	0.172
Manapal/WT (break)	1.35725	0.14
Manapal/WT (red)	0.92654	0.424