Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.1.4.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22645	0.755
27DAP/17DAP	0.79671	0.491
39DAP/27DAP	0.99253	0.798
41DAP/39DAP	1.0953	0.797
42DAP/41DAP	1.13136	0.844
43DAP/42DAP	0.92596	0.846
47DAP/43DAP	0.92434	0.716
52DAP/47DAP	1.07589	0.91
57DAP/52DAP	1.53493	0.817

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78311	0.064
17DAP/reference	0.95189	0.448
27DAP/reference	0.9285	0.223
39DAP/reference	0.97361	0.691
41DAP/reference	0.89134	0.154
42DAP/reference	0.8262	0.003
43DAP/reference	0.97957	0.675
47DAP/reference	0.93691	0.224
52DAP/reference	1.0564	0.498
57DAP/reference	1.07328	0.066

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04363	0.87
27DAP/17DAP	1.13626	0.735
39DAP/27DAP	0.80154	0.044
41DAP/39DAP	1.05398	1
42DAP/41DAP	1.22772	0.225
43DAP/42DAP	0.64078	0.023
47DAP/43DAP	0.96105	0.843
52DAP/47DAP	1.14521	0.624
57DAP/52DAP	0.91316	0.555
57DAP/7DAP	0.80798	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29313	0.121
17DAP/reference	1.07172	0.896
27DAP/reference	0.97582	0.494
39DAP/reference	1.21078	0.114
41DAP/reference	1.03238	0.949
42DAP/reference	0.89507	0.222
43DAP/reference	1.04502	1
47DAP/reference	0.92247	0.383
52DAP/reference	0.81948	0.09
57DAP/reference	0.87128	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03254	0.93
17DAP/reference	0.86038	0.092
27DAP/reference	0.9211	0.195
39DAP/reference	1.03541	1
41DAP/reference	1.24217	0.081
42DAP/reference	0.91556	0.261
43DAP/reference	0.72453	0.017
47DAP/reference	0.84899	0.087
52DAP/reference	0.96406	0.407
57DAP/reference	0.87173	0.226

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06387	1
17DAP/reference	0.97303	0.636
27DAP/reference	1.04026	0.834
39DAP/reference	0.84808	0.083
41DAP/reference	0.83281	0.096
42DAP/reference	1.04108	0.848
43DAP/reference	0.84528	0.098
47DAP/reference	0.91409	0.24
52DAP/reference	1.04081	0.928
57DAP/reference	0.97402	0.543

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13469	0.966
26DAP/20DAP	0.81395	0.317
34DAP/26DAP	0.614	0.111
51DAP/34DAP	0.43841	0.049
52DAP/51DAP	0.94739	1
53DAP/52DAP	1.00709	0.97
55DAP/53DAP	0.94636	0.632
57DAP/55DAP	1.03071	0.97
62DAP/57DAP	1.06078	0.767
68DAP/62DAP	1.96756	0.21
68DAP/14DAP	0.75319	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.2917	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.92393	0.287
Mature Green Tomato/Ripe Tomato	7.17473	0.015
Immature Eggplant/Mature Eggplant	0.77776	0.092
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	23.0051	0.26

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	0.8757	N/A
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	1.07382	N/A
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	N/A	N/A
IL2-6/WTpooled	1.03452	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97778	1
IL12-4/WTpooled	0.84325	0.52
IL1-4/WTpooled	1.22349	N/A
WT/WTpooled	0.95567	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	0.87761	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.83117	1
DC3000/delta hrp 6h	1.0708	1
DC3000/delta hrp 12h	1.23501	1
DC3000/delta hrp 24h	0.85764	0.346

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94082	1
Exp 36h	0.95395	0.943
Exp 60h	0.94957	0.664

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.01677	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.1779	0.286
transgenic ySAMdc/azygous control (breaker)	0.90807	0.49
transgenic ySAMdc/azygous control (red)	0.88984	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.2911	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97377	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.53341	0.172
Manapal/WT (break)	0.88583	1
Manapal/WT (red)	0.85099	0.242