Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73689	0.182
27DAP/17DAP	1.14117	0.872
39DAP/27DAP	0.80807	0.549
41DAP/39DAP	0.81662	0.412
42DAP/41DAP	1.04344	1
43DAP/42DAP	0.90375	0.827
47DAP/43DAP	1.87528	0.349
52DAP/47DAP	1.23913	0.645
57DAP/52DAP	1.00978	0.985

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78708	0.035
17DAP/reference	1.01593	0.696
27DAP/reference	1.04545	0.672
39DAP/reference	1.03626	0.654
41DAP/reference	1.05845	0.421
42DAP/reference	0.9592	0.134
43DAP/reference	0.9157	0.118
47DAP/reference	1.04473	0.318
52DAP/reference	0.9243	0.177
57DAP/reference	1.11488	0.3

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08582	0.87
27DAP/17DAP	0.94944	0.854
39DAP/27DAP	0.90699	0.556
41DAP/39DAP	1.1491	0.603
42DAP/41DAP	0.9961	0.91
43DAP/42DAP	1.01832	1
47DAP/43DAP	1.19751	0.798
52DAP/47DAP	0.83943	0.538
57DAP/52DAP	1.15702	0.574
57DAP/7DAP	0.73354	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96441	0.361
17DAP/reference	0.98959	0.599
27DAP/reference	1.17113	0.017
39DAP/reference	0.94813	0.264
41DAP/reference	1.08994	0.325
42DAP/reference	0.97847	0.554
43DAP/reference	1.05616	0.764
47DAP/reference	1.07649	0.304
52DAP/reference	1.42449	0.048
57DAP/reference	1.4374	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87875	0.157
17DAP/reference	0.9416	0.287
27DAP/reference	0.96676	0.519
39DAP/reference	0.91402	0.132
41DAP/reference	1.01111	0.749
42DAP/reference	1.02185	1
43DAP/reference	1.04193	0.863
47DAP/reference	1.07	0.467
52DAP/reference	0.87612	0.093
57DAP/reference	0.87659	0.043

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92019	0.268
17DAP/reference	0.96923	0.571
27DAP/reference	0.93392	0.155
39DAP/reference	0.96941	0.299
41DAP/reference	0.95202	0.331
42DAP/reference	0.93033	0.361
43DAP/reference	0.93877	0.226
47DAP/reference	1.17486	0.032
52DAP/reference	1.03954	0.89
57DAP/reference	1.05323	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.13111	0.966
26DAP/20DAP	0.92359	1
34DAP/26DAP	1.0446	1
51DAP/34DAP	2.55523	0.159
52DAP/51DAP	0.87206	1
53DAP/52DAP	1.04354	0.783
55DAP/53DAP	1.14975	0.755
57DAP/55DAP	0.84175	0.246
62DAP/57DAP	0.84336	0.466
68DAP/62DAP	1.38812	0.193
68DAP/14DAP	1.16915	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27703	0.496

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.94782	0.044
Immature Eggplant/Mature Eggplant	0.75525
Ripe Pepper/Ripe Tomato	0.91379	1
Mature Eggplant/Ripe Tomato	0.37932	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.59446
12-2/M82	0.95406	1
12-4/M82	0.85159
1-3/M82	N/A	N/A
2-1-1/M82	1.37287
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	1.09095	1
4-1/M82	N/A	N/A
4-3-2/M82	0.90974
4-3/M82	0.64146
5-3/M82	1.60894
6-2/M82	1.16977
6-3/M82	1.12368
7-1/M82	1.54549
7-2/M82	0.3801
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93942	1
IL2-6/WTpooled	1.25303	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.25518	1
IL12-4/WTpooled	1.16903	0.839
IL1-4/WTpooled	0.98087	1
WT/WTpooled	1.01748	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	0.75452

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.1363	0.921
DC3000/delta hrp 6h	1.07326	1
DC3000/delta hrp 12h	1.03251	1
DC3000/delta hrp 24h	1.18763	0.582

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	1.05173	1
Exp 36h	0.65216	0.406
Exp 60h	0.60891	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02983	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.82779	0.613
Var 12h NI row2-row1	1.76201	1
Var 36h I row2-row1	1.08587	0.489
Var 36h NI row2-row1	0.94565
Var 60h I row2-row1	0.99335	1
Var 60h NI row2-row1	0.80047
Time course 0hI-0hNI	1.23819	0.662
Time course 12hI-12hNI	0.77361	0.201
Time course 36hI-36hNI	1.27386	0.453
Time course 60hI-60hNI	1.40129	0.187

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)	0.96045	0.391
transgenic ySAMdc/azygous control (breaker)	0.88198	0.251
transgenic ySAMdc/azygous control (red)	1.04528	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98738	0.534

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.45961	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38387	0.105
Manapal/WT (break)	1.18327	0.381
Manapal/WT (red)	1.35418	0.413