Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78137	0.413
27DAP/17DAP	1.30473	0.755
39DAP/27DAP	1.45396	0.575
41DAP/39DAP	0.90451	0.63
42DAP/41DAP	1.58742	0.471
43DAP/42DAP	0.76771	0.483
47DAP/43DAP	1.9799	0.173
52DAP/47DAP	0.82031	0.54
57DAP/52DAP	1.03645	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96238	0.55
17DAP/reference	1.05853	0.717
27DAP/reference	1.3752	0.061
39DAP/reference	1.77392	0.066
41DAP/reference	1.45385	0.241
42DAP/reference	1.3442	0.01
43DAP/reference	1.75673	0.812
47DAP/reference	1.56627	0.001
52DAP/reference	1.62428	0.092
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.3747	0.164
27DAP/17DAP	0.89134	0.748
39DAP/27DAP	3.22905	0.034
41DAP/39DAP	0.41325	0.016
42DAP/41DAP	2.23826	0.002
43DAP/42DAP	2.17407	0.014
47DAP/43DAP	1.00264	0.99
52DAP/47DAP	0.63479	0.05
57DAP/52DAP	0.70863	0.082
57DAP/7DAP	0.63142

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83278	0.076
17DAP/reference	0.72727	0.012
27DAP/reference	0.81707	0.03
39DAP/reference	0.79401	0.015
41DAP/reference	0.68632	0.014
42DAP/reference	0.82755	0.034
43DAP/reference	1.08745	0.511
47DAP/reference	1.33651	0.031
52DAP/reference	1.07756	0.491
57DAP/reference	0.82391	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76988	0.01
17DAP/reference	0.72166	0.006
27DAP/reference	0.75106	0.06
39DAP/reference	0.93917	0.381
41DAP/reference	0.7465	0.056
42DAP/reference	0.96603	0.482
43DAP/reference	0.87578	0.152
47DAP/reference	0.99402	0.609
52DAP/reference	0.85203	0.04
57DAP/reference	0.7171	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83336	0.054
17DAP/reference	0.83399	0.13
27DAP/reference	0.81128	0.042
39DAP/reference	0.99846	0.819
41DAP/reference	1.00681	1
42DAP/reference	1.31569	0.033
43DAP/reference	1.57569	0.022
47DAP/reference	1.20108	0.031
52DAP/reference	1.46478	0.059
57DAP/reference	1.14923	0.744

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99122	1
26DAP/20DAP	1.18294	1
34DAP/26DAP	1.38711	1
51DAP/34DAP	1.22168	0.98
52DAP/51DAP	1.04505	1
53DAP/52DAP	0.77025	0.64
55DAP/53DAP	1.37713	0.645
57DAP/55DAP	0.78896	0.499
62DAP/57DAP	1.3082	0.515
68DAP/62DAP	1.42336	0.367
68DAP/14DAP	2.81627	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	9.75535	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.02666
Mature Green Tomato/Ripe Tomato	0.74189	0.042
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.06323
Mature Eggplant/Ripe Tomato	0.07892	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.75961	0.877
1-1-2/M82	1.1913	1
12-2/M82	1.42913
12-4/M82	1.05644	1
1-3/M82	2.36743	0.26
2-1-1/M82	1.10772	0.366
2-1/M82	0.86296	0.345
2-6/M82	1.25574	0.425
3-2/M82	1.35023	0.967
4-1-1/M82	1.40389	1
4-1/M82	1.89642	0.853
4-3-2/M82	1.08613	0.262
4-3/M82	1.35433	1
5-3/M82	0.83704	0.49
6-2/M82	0.23113	0.481
6-3/M82	1.06665	1
7-1/M82	0.85865	0.803
7-2/M82	1.63741	0.324
9-3-2/M82	1.48258	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1886	0.277
IL2-6/WTpooled	0.58839	0.383
IL7-5/WTpooled	1.15863	0.6
IL7-3/WTpooled	1.16076	1
IL12-4/WTpooled	1.13928	0.737
IL1-4/WTpooled	0.87052	0.476
WT/WTpooled	1.02377	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	1.01777	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06221	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.09869	1
DC3000/delta hrp 24h	1.18504	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.31995
DC3000 delta B/DC3000 delta AB	0.95538	0.657

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	1.64553
Var 0h	N/A	N/A
Var 12h I row2-row1	0.49393
Var 12h NI row2-row1	0.53892
Var 36h I row2-row1	0.86975
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	2.04012	0.904
Time course 0hI-0hNI	1.20301
Time course 12hI-12hNI	1.08773	1
Time course 36hI-36hNI	8.74101	0.975
Time course 60hI-60hNI	0.65655	0.319

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)	0.75222	0.246
transgenic ySAMdc/azygous control (breaker)	0.95372	1
transgenic ySAMdc/azygous control (red)	0.79195	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2286	0.148

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97209	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98116	1
Manapal/WT (break)	0.91346	1
Manapal/WT (red)	1.19619	0.413