Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.1.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94584	0.586
27DAP/17DAP	0.73152	0.345
39DAP/27DAP	0.95676	0.7
41DAP/39DAP	1.02626	0.871
42DAP/41DAP	1.27833	0.39
43DAP/42DAP	0.7909	0.554
47DAP/43DAP	1.02575	0.95
52DAP/47DAP	1.50253	0.538
57DAP/52DAP	1.23474	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.79713	0.03
17DAP/reference	0.74151	0.008
27DAP/reference	0.95337	0.265
39DAP/reference	0.81604	0.035
41DAP/reference	0.73751	0.049
42DAP/reference	1.03163	0.707
43DAP/reference	0.97949	0.728
47DAP/reference	0.99633	0.602
52DAP/reference	1.03854	0.695
57DAP/reference	1.11058	0.239

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24061	0.438
27DAP/17DAP	0.94673	0.854
39DAP/27DAP	0.89345	0.367
41DAP/39DAP	1.22593	0.774
42DAP/41DAP	0.7019	0.032
43DAP/42DAP	1.02955	0.83
47DAP/43DAP	0.90684	0.734
52DAP/47DAP	0.94163	0.837
57DAP/52DAP	0.91965	0.591
57DAP/7DAP	0.84383

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91116	0.224
17DAP/reference	0.88856	0.167
27DAP/reference	1.10791	0.804
39DAP/reference	0.91507	0.198
41DAP/reference	0.9079	0.235
42DAP/reference	1.11313	0.889
43DAP/reference	1.1172	0.325
47DAP/reference	0.9787	0.671
52DAP/reference	0.80249	0.043
57DAP/reference	1.19029	0.799

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95899	0.607
17DAP/reference	0.80072	0.021
27DAP/reference	1.00912	1
39DAP/reference	1.01742	1
41DAP/reference	1.13067	0.228
42DAP/reference	0.98756	0.594
43DAP/reference	0.7871	0.033
47DAP/reference	0.84173	0.018
52DAP/reference	1.05314	0.559
57DAP/reference	0.8483	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06734	0.775
17DAP/reference	0.87558	0.342
27DAP/reference	0.85727	0.06
39DAP/reference	1.06743	0.218
41DAP/reference	0.88605	0.237
42DAP/reference	0.95645	0.671
43DAP/reference	1.1541	0.445
47DAP/reference	0.85694	0.093
52DAP/reference	1.04623	0.854
57DAP/reference	1.1396	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13484	1
26DAP/20DAP	1.07036	0.798
34DAP/26DAP	1.09856	1
51DAP/34DAP	1.09489	0.949
52DAP/51DAP	0.80551	1
53DAP/52DAP	1.28386	0.502
55DAP/53DAP	0.9179	0.632
57DAP/55DAP	1.18812	0.841
62DAP/57DAP	1.11306	0.833
68DAP/62DAP	1.24048	0.557
68DAP/14DAP	2.07275	0.074

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74366	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.03038	0.058
Mature Green Tomato/Ripe Tomato	3.07517	0.267
Immature Eggplant/Mature Eggplant	1.25309	0.417
Ripe Pepper/Ripe Tomato	3.97176	0.258
Mature Eggplant/Ripe Tomato	0.90933	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.70761
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.09216
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.32623	0.277
IL2-6/WTpooled	1.06226	1
IL7-5/WTpooled	0.78359	1
IL7-3/WTpooled	1.18541	1
IL12-4/WTpooled	1.1243	0.595
IL1-4/WTpooled	1.00796	1
WT/WTpooled	1.1575	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	0.95653	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.12642	0.914
DC3000/delta hrp 6h	1.13382	1
DC3000/delta hrp 12h	0.9859	1
DC3000/delta hrp 24h	1.03725	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	1.03346	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9028	1
Exp 36h	1.04032	1
Exp 60h	0.92044	0.754

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00422	1
Var 0h	0.71722	1
Var 12h I row2-row1	1.01381	1
Var 12h NI row2-row1	0.93043	0.906
Var 36h I row2-row1	0.98835	1
Var 36h NI row2-row1	0.5278	1
Var 60h I row2-row1	1.14877
Var 60h NI row2-row1	0.87283	0.691
Time course 0hI-0hNI	0.92655	0.309
Time course 12hI-12hNI	1.06073	0.818
Time course 36hI-36hNI	0.82447	0.062
Time course 60hI-60hNI	0.46821	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)	1.00432	0.921
transgenic ySAMdc/azygous control (breaker)	0.912	0.251
transgenic ySAMdc/azygous control (red)	0.96064	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02518	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.81694	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.96722	1
Manapal/WT (red)	0.9724	0.863