Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.13.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09524	0.798
27DAP/17DAP	1.13696	0.881
39DAP/27DAP	0.78938	0.435
41DAP/39DAP	1.49078	0.387
42DAP/41DAP	0.9395	1
43DAP/42DAP	1.05177	1
47DAP/43DAP	1.11027	0.746
52DAP/47DAP	1.30412	0.559
57DAP/52DAP	0.87924	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01752	0.994
17DAP/reference	1.04122	0.294
27DAP/reference	1.01661	0.831
39DAP/reference	1.14645	0.445
41DAP/reference	1.0877	0.058
42DAP/reference	0.97179	0.218
43DAP/reference	1.0259	0.547
47DAP/reference	0.96037	0.191
52DAP/reference	0.9059	0.147
57DAP/reference	0.93306	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0082	1
27DAP/17DAP	0.99019	0.887
39DAP/27DAP	1.10542	0.369
41DAP/39DAP	1.00308	1
42DAP/41DAP	0.99912	0.902
43DAP/42DAP	1.01379	0.788
47DAP/43DAP	1.01923	0.906
52DAP/47DAP	1.01563	0.979
57DAP/52DAP	1.02236	0.877
57DAP/7DAP	1.10776	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95146	0.55
17DAP/reference	0.97682	0.338
27DAP/reference	0.97549	0.348
39DAP/reference	0.92702	0.025
41DAP/reference	0.84332	0.029
42DAP/reference	0.87549	0.011
43DAP/reference	0.88705	0.126
47DAP/reference	0.92619	0.101
52DAP/reference	0.91252	0.126
57DAP/reference	0.85684	0.034

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99862	0.907
17DAP/reference	0.95726	0.208
27DAP/reference	0.98258	0.576
39DAP/reference	0.98648	0.554
41DAP/reference	1.17034	0.416
42DAP/reference	1.0647	0.697
43DAP/reference	1.20618	0.173
47DAP/reference	1.03927	0.589
52DAP/reference	0.97897	0.469
57DAP/reference	1.11756	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94154	0.135
17DAP/reference	1.01568	0.784
27DAP/reference	1.02476	0.552
39DAP/reference	0.96404	0.179
41DAP/reference	0.97972	0.56
42DAP/reference	0.88525	0.049
43DAP/reference	0.93671	0.081
47DAP/reference	0.94637	0.348
52DAP/reference	0.93238	0.376
57DAP/reference	0.81094	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03943	0.966
26DAP/20DAP	0.94241	1
34DAP/26DAP	1.0138	1
51DAP/34DAP	1.03489	0.746
52DAP/51DAP	1.06744	0.295
53DAP/52DAP	0.98288	0.902
55DAP/53DAP	1.01812	0.964
57DAP/55DAP	1.05082	0.975
62DAP/57DAP	1.08815	0.678
68DAP/62DAP	1.08	0.885
68DAP/14DAP	1.08602	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98565	0.635

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.99802	0.898
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.77466	0.293
Mature Eggplant/Ripe Tomato	0.43032	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03489	1
1-1-2/M82	1.03103	1
12-2/M82	1.44904
12-4/M82	0.95129	1
1-3/M82	0.90605	0.441
2-1-1/M82	1.15617
2-1/M82	1.53064	0.345
2-6/M82	0.98287	1
3-2/M82	0.88669
4-1-1/M82	1.1147	1
4-1/M82	0.90646	1
4-3-2/M82	0.86626	0.487
4-3/M82	1.06698	1
5-3/M82	0.97631	1
6-2/M82	0.96352	1
6-3/M82	0.97027	1
7-1/M82	0.91566
7-2/M82	1.06844	0.282
9-3-2/M82	0.92523	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99163	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01299
IL12-4/WTpooled	0.75655	0.543
IL1-4/WTpooled	0.87994	0.834
WT/WTpooled	1.08716	0.874

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	0.95612	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90013	1
DC3000/delta hrp 6h	0.82198	0.95
DC3000/delta hrp 12h	1.15374	1
DC3000/delta hrp 24h	1.08912	0.502

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03996	0.476
DC3000 delta B/DC3000 delta AB	1.10628	0.449

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06781	1
Exp 36h	N/A	N/A
Exp 60h	1.25898	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00052	1
Var 0h	1.27806	0.98
Var 12h I row2-row1	1.74308	0.263
Var 12h NI row2-row1	0.94157	0.82
Var 36h I row2-row1	1.01467	1
Var 36h NI row2-row1	0.92151	0.743
Var 60h I row2-row1	1.11187	1
Var 60h NI row2-row1	1.21045	0.904
Time course 0hI-0hNI	1.10286	0.799
Time course 12hI-12hNI	1.07732	0.663
Time course 36hI-36hNI	0.96588	0.337
Time course 60hI-60hNI	1.37781	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)	0.91975	0.246
transgenic ySAMdc/azygous control (breaker)	1.26706	0.172
transgenic ySAMdc/azygous control (red)	0.98579	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01416	0.471

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.8705	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01206	1
Manapal/WT (break)	0.81143	0.333
Manapal/WT (red)	0.79713	0.315