Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77504	0.29
27DAP/17DAP	1.36978	0.809
39DAP/27DAP	1.1036	0.876
41DAP/39DAP	0.9484	0.752
42DAP/41DAP	1.19309	0.916
43DAP/42DAP	0.93419	0.877
47DAP/43DAP	0.78348	0.345
52DAP/47DAP	1.4104	0.619
57DAP/52DAP	1.24054	0.843

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43349	1
17DAP/reference	0.73721
27DAP/reference	0.50264
39DAP/reference	N/A	N/A
41DAP/reference	N/A	N/A
42DAP/reference	0.77494	0.085
43DAP/reference	0.68066
47DAP/reference	0.79571	0.011
52DAP/reference	N/A	N/A
57DAP/reference	0.65521

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89851	0.509
27DAP/17DAP	0.90267	0.821
39DAP/27DAP	1.55476	0.343
41DAP/39DAP	1.77999	0.781
42DAP/41DAP	0.94638	0.721
43DAP/42DAP	0.96971	0.751
47DAP/43DAP	1.10457	0.941
52DAP/47DAP	0.89233	0.739
57DAP/52DAP	1.31672	0.925
57DAP/7DAP	1.14565	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9392	0.27
17DAP/reference	1.09234	0.822
27DAP/reference	0.95436	0.264
39DAP/reference	1.09222	0.74
41DAP/reference	0.89948	0.271
42DAP/reference	0.78823	0.086
43DAP/reference	1.35231	0.02
47DAP/reference	0.86536	0.168
52DAP/reference	0.97161	0.477
57DAP/reference	0.86662	0.27

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75871	0.079
17DAP/reference	0.70182	0.041
27DAP/reference	0.70312	0.173
39DAP/reference	0.70215	0.03
41DAP/reference	0.80048	0.145
42DAP/reference	0.7513	0.017
43DAP/reference	0.68499	0.017
47DAP/reference	0.79002	0.012
52DAP/reference	0.70486	0.005
57DAP/reference	0.65186	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99429	0.75
17DAP/reference	0.84584	0.121
27DAP/reference	0.95754	0.465
39DAP/reference	0.92419	0.271
41DAP/reference	0.98518	0.682
42DAP/reference	1.05363	0.701
43DAP/reference	1.26581	0.388
47DAP/reference	0.82852	0.052
52DAP/reference	1.08362	1
57DAP/reference	2.07989	0.214

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31989	0.966
26DAP/20DAP	1.14954	1
34DAP/26DAP	0.67812	0.161
51DAP/34DAP	1.26411	0.121
52DAP/51DAP	1.24977	0.954
53DAP/52DAP	1.00284	0.929
55DAP/53DAP	0.95162	0.735
57DAP/55DAP	0.69889	0.282
62DAP/57DAP	1.14474	0.723
68DAP/62DAP	1.65331	0.087
68DAP/14DAP	1.55094	0.236

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47201	0.186

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.03009	0.948
Immature Eggplant/Mature Eggplant	2.66785	0.05
Ripe Pepper/Ripe Tomato	1.57608
Mature Eggplant/Ripe Tomato	1.48162

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	1.1525
12-4/M82	N/A	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	1.52759
4-3-2/M82	N/A	N/A
4-3/M82	0.6782
5-3/M82	1.04247
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	1.08276	0.365
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.05276	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.19202	1
WT/WTpooled	N/A	N/A

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	1.20929	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01544	1
DC3000/delta hrp 6h	1.15271	1
DC3000/delta hrp 12h	1.04663	1
DC3000/delta hrp 24h	1.13785	0.553

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	1.66899	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05524	1
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	2.05232
Var 0h	N/A	N/A
Var 12h I row2-row1	4.2466	0.296
Var 12h NI row2-row1	1.48758	0.649
Var 36h I row2-row1	0.39957
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.66714	0.285
Var 60h NI row2-row1	0.42621	0.977
Time course 0hI-0hNI	6.30467	0.799
Time course 12hI-12hNI	1.80909	0.714
Time course 36hI-36hNI	1.94405	0.453
Time course 60hI-60hNI	1.15284	0.08

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	1.37403	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.52265	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.18592	0.307
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.70008	0.274