Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.10.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.4447	0.076
27DAP/17DAP	1.77997	0.479
39DAP/27DAP	1.69981	0.187
41DAP/39DAP	0.91108	0.636
42DAP/41DAP	1.62768	0.466
43DAP/42DAP	0.79945	0.467
47DAP/43DAP	1.00082	0.934
52DAP/47DAP	0.74162	0.32
57DAP/52DAP	0.95331	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0417	0.814
17DAP/reference	1.1071	0.427
27DAP/reference	1.17504	0.179
39DAP/reference	1.16616	0.051
41DAP/reference	0.90842	0.085
42DAP/reference	1.03125	0.656
43DAP/reference	1.07448	0.73
47DAP/reference	1.27973	0.002
52DAP/reference	1.21631	0.043
57DAP/reference	1.21095	0.063

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18889	0.326
27DAP/17DAP	1.09123	0.754
39DAP/27DAP	1.30346	0.224
41DAP/39DAP	1.32939	0.393
42DAP/41DAP	0.93931	0.61
43DAP/42DAP	0.82723	0.079
47DAP/43DAP	1.14948	0.344
52DAP/47DAP	0.8735	0.366
57DAP/52DAP	0.99134	0.841
57DAP/7DAP	1.33064	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34662	0.078
17DAP/reference	1.2536	0.007
27DAP/reference	1.32148	0.01
39DAP/reference	1.16037	0.025
41DAP/reference	1.19747	0.077
42DAP/reference	1.20978	0.021
43DAP/reference	1.28849	0.011
47DAP/reference	1.37833	0.07
52DAP/reference	1.4799	0.007
57DAP/reference	1.42876	0.02

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9516	0.592
17DAP/reference	0.92179	0.07
27DAP/reference	0.85855	0.249
39DAP/reference	1.11342	0.62
41DAP/reference	1.03092	1
42DAP/reference	0.90841	0.212
43DAP/reference	1.19481	0.929
47DAP/reference	1.41731	0.036
52DAP/reference	0.95154	0.239
57DAP/reference	1.2981	0.062

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28813	0.051
17DAP/reference	1.0151	0.9
27DAP/reference	1.14138	0.131
39DAP/reference	1.29163	0.05
41DAP/reference	1.16532	0.134
42DAP/reference	1.42272	0.01
43DAP/reference	1.20987	0.128
47DAP/reference	1.19138	0.104
52DAP/reference	1.38562	0.116
57DAP/reference	1.19573	0.157

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90191	0.997
26DAP/20DAP	0.93303	1
34DAP/26DAP	0.85243	0.272
51DAP/34DAP	1.87053	0.033
52DAP/51DAP	0.88498	1
53DAP/52DAP	1.05889	0.935
55DAP/53DAP	0.7761	0.088
57DAP/55DAP	1.59193	0.222
62DAP/57DAP	1.59018	0.445
68DAP/62DAP	1.04948	1
68DAP/14DAP	1.1969	0.694

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31752	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.33104	0.077
Mature Green Tomato/Ripe Tomato	0.94439	0.715
Immature Eggplant/Mature Eggplant	1.66433	0.05
Ripe Pepper/Ripe Tomato	1.47558	0.256
Mature Eggplant/Ripe Tomato	0.57514	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26589	0.574
1-1-2/M82	1.46458	1
12-2/M82	0.98525
12-4/M82	0.84424	0.319
1-3/M82	2.31454
2-1-1/M82	N/A	N/A
2-1/M82	1.17117
2-6/M82	1.14529	0.505
3-2/M82	1.32303
4-1-1/M82	1.35872
4-1/M82	0.74536
4-3-2/M82	1.36151	0.284
4-3/M82	1.80685	0.268
5-3/M82	1.21302	0.572
6-2/M82	2.25896
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	1.53533	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19535	0.365
IL2-6/WTpooled	0.66362	0.348
IL7-5/WTpooled	0.91796	1
IL7-3/WTpooled	1.22721	0.362
IL12-4/WTpooled	1.09981	0.646
IL1-4/WTpooled	0.9807	1
WT/WTpooled	1.02365	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	1.20115	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97299
DC3000/delta hrp 6h	1.06657	1
DC3000/delta hrp 12h	1.18464	1
DC3000/delta hrp 24h	0.93246	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.42451	0.043
DC3000 delta B/DC3000 delta AB	1.31019	0.17

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.18347	0.196
Exp 36h	1.64336	0.326
Exp 60h	2.10971	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05574	1
Var 0h	0.98027	1
Var 12h I row2-row1	1.18083	0.224
Var 12h NI row2-row1	1.35752	0.34
Var 36h I row2-row1	1.26668	0.304
Var 36h NI row2-row1	0.82038	0.61
Var 60h I row2-row1	0.6969	0.306
Var 60h NI row2-row1	0.84702	0.431
Time course 0hI-0hNI	1.11204	0.344
Time course 12hI-12hNI	1.6113	0.005
Time course 36hI-36hNI	2.87159	0.004
Time course 60hI-60hNI	7.36987	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)	0.94813	0.348
transgenic ySAMdc/azygous control (breaker)	0.95583	1
transgenic ySAMdc/azygous control (red)	0.90888	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10457	0.119

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78158	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.11366	1
Manapal/WT (break)	0.79966	0.333
Manapal/WT (red)	0.73509	0.187