Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.16.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.44566	0.588
27DAP/17DAP	2.71088	0.087
39DAP/27DAP	4.20485	0.395
41DAP/39DAP	2.08192	0.432
42DAP/41DAP	1.00652	1
43DAP/42DAP	1.46664	1
47DAP/43DAP	0.15664	0.032
52DAP/47DAP	0.9969	0.806
57DAP/52DAP	1.06334	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62073	0.027
17DAP/reference	0.66812	0.008
27DAP/reference	0.97659	0.654
39DAP/reference	0.76623	0.093
41DAP/reference	0.78181	0.154
42DAP/reference	1.70407	0.007
43DAP/reference	0.76344	0.047
47DAP/reference	0.84384	0.008
52DAP/reference	0.86243	0.223
57DAP/reference	0.961	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8427	0.27
27DAP/17DAP	1.13477	0.65
39DAP/27DAP	5.89387	0.046
41DAP/39DAP	5.44993	0.005
42DAP/41DAP	0.60115	0.007
43DAP/42DAP	0.30668	0.02
47DAP/43DAP	1.09409	0.873
52DAP/47DAP	1.49484	0.987
57DAP/52DAP	0.90027	0.466
57DAP/7DAP	0.94623	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62708	0.06
17DAP/reference	1.7433	0.147
27DAP/reference	2.27071	0.301
39DAP/reference	2.17189	0.198
41DAP/reference	0.76843	0.037
42DAP/reference	1.76817	0.405
43DAP/reference	1.08389	0.608
47DAP/reference	2.2375	0.055
52DAP/reference	2.04538	0.013
57DAP/reference	2.5	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.56918	0.007
17DAP/reference	0.84296	0.116
27DAP/reference	0.87969	0.097
39DAP/reference	2.23087	0.15
41DAP/reference	1.63628	0.015
42DAP/reference	1.6604	0.185
43DAP/reference	3.01566	0.037
47DAP/reference	3.75543	0.016
52DAP/reference	1.33125	0.061
57DAP/reference	4.26776	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87767	0.268
17DAP/reference	1.49859	0.496
27DAP/reference	0.8971	0.065
39DAP/reference	1.62955	0.035
41DAP/reference	1.75053	0.074
42DAP/reference	0.77464	0.172
43DAP/reference	0.66711	0.042
47DAP/reference	0.59423	0.005
52DAP/reference	0.61234	0.049
57DAP/reference	0.89848	0.208

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97244	1
26DAP/20DAP	0.75326	1
34DAP/26DAP	2.17181	1
51DAP/34DAP	1.06962	0.911
52DAP/51DAP	1.01866	1
53DAP/52DAP	0.60265	0.386
55DAP/53DAP	0.92423	0.746
57DAP/55DAP	0.81515	0.433
62DAP/57DAP	1.39048	0.678
68DAP/62DAP	0.79338	0.505
68DAP/14DAP	1.00021	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	6.1264	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	12.1802	0.015
Immature Eggplant/Mature Eggplant	49.362
Ripe Pepper/Ripe Tomato	0.18273
Mature Eggplant/Ripe Tomato	0.19007

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.44103
1-1-2/M82	1.56385	1
12-2/M82	1.23923	1
12-4/M82	1.48347	1
1-3/M82	1.94748	0.277
2-1-1/M82	0.71105	0.465
2-1/M82	5.39699
2-6/M82	1.41857	0.329
3-2/M82	N/A	N/A
4-1-1/M82	3.51042	0.876
4-1/M82	1.10691
4-3-2/M82	5.56454	0.508
4-3/M82	1.07833
5-3/M82	1.99063	0.572
6-2/M82	15.2244	0.235
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.98712	0.299
9-3-2/M82	3.32622	0.196

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.79219
WT/WTpooled	1.18647

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	1.76163	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00749	1
DC3000/delta hrp 6h	1.13196	0.533
DC3000/delta hrp 12h	0.97351	1
DC3000/delta hrp 24h	3.11612	0.025

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.24888	0.042
DC3000 delta B/DC3000 delta AB	4.47726	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.9582	0.254
Exp 36h	1.36157	1
Exp 60h	2.59621	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02182	1
Var 0h	0.95026	1
Var 12h I row2-row1	1.08825	0.544
Var 12h NI row2-row1	2.86711	0.191
Var 36h I row2-row1	1.32982	0.41
Var 36h NI row2-row1	0.5158	0.522
Var 60h I row2-row1	1.00311	1
Var 60h NI row2-row1	0.62153	0.483
Time course 0hI-0hNI	2.00339	0.662
Time course 12hI-12hNI	1.95765	0.493
Time course 36hI-36hNI	10.5763	0.004
Time course 60hI-60hNI	95.1124	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)	0.3459	0.246
transgenic ySAMdc/azygous control (breaker)	0.5908	0.15
transgenic ySAMdc/azygous control (red)	1.02812	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97811	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.11301	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.46173	0.14
Manapal/WT (break)	0.40532	0.333
Manapal/WT (red)	0.61835	0.607