Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.9.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.43253	0.106
27DAP/17DAP	0.92117	0.827
39DAP/27DAP	1.61811	0.14
41DAP/39DAP	0.87464	0.499
42DAP/41DAP	1.68024	0.107
43DAP/42DAP	1.19974	0.923
47DAP/43DAP	0.81143	0.42
52DAP/47DAP	0.68129	0.218
57DAP/52DAP	1.06923	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.73881	0.012
17DAP/reference	1.09992	0.22
27DAP/reference	1.19311	0.084
39DAP/reference	1.08897	0.524
41DAP/reference	0.92144	0.341
42DAP/reference	1.08821	0.013
43DAP/reference	1.03436	0.705
47DAP/reference	0.85783	0.137
52DAP/reference	0.81292	0.05
57DAP/reference	0.86769	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.83448	0.036
27DAP/17DAP	0.87382	0.648
39DAP/27DAP	1.33124	0.373
41DAP/39DAP	0.78714	0.372
42DAP/41DAP	1.28016	0.273
43DAP/42DAP	1.19727	0.351
47DAP/43DAP	0.89226	0.325
52DAP/47DAP	0.83254	0.304
57DAP/52DAP	0.66521	0.189
57DAP/7DAP	0.98567	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19394	0.053
17DAP/reference	1.00284	1
27DAP/reference	0.82295	0.024
39DAP/reference	0.78125	0.031
41DAP/reference	0.65525	0.02
42DAP/reference	0.64123	0.023
43DAP/reference	0.57517	0.01
47DAP/reference	0.779	0.128
52DAP/reference	0.62752	0.012
57DAP/reference	0.63619	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23935	0.033
17DAP/reference	1.37506	0.031
27DAP/reference	1.22037	0.045
39DAP/reference	1.23943	0.366
41DAP/reference	1.31593	0.309
42DAP/reference	1.1626	0.096
43DAP/reference	1.2318	0.107
47DAP/reference	1.04499	0.353
52DAP/reference	0.8384	0.121
57DAP/reference	0.83478	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.04002	0.015
17DAP/reference	1.60803	0.126
27DAP/reference	1.30989	0.02
39DAP/reference	1.11503	0.264
41DAP/reference	1.04689	0.84
42DAP/reference	0.97086	0.671
43DAP/reference	1.04322	0.79
47DAP/reference	1.17123	0.155
52DAP/reference	0.98881	0.718
57DAP/reference	1.11021	0.285

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08504	0.966
26DAP/20DAP	0.77421	0.317
34DAP/26DAP	0.96799	0.944
51DAP/34DAP	1.30651	0.159
52DAP/51DAP	0.89953	1
53DAP/52DAP	1.04149	0.961
55DAP/53DAP	0.61638	0.031
57DAP/55DAP	0.85661	0.318
62DAP/57DAP	2.76369	0.034
68DAP/62DAP	0.88943	0.722
68DAP/14DAP	0.65621	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.67429	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.64975	0.058
Mature Green Tomato/Ripe Tomato	2.22567	0.016
Immature Eggplant/Mature Eggplant	0.46417	0.063
Ripe Pepper/Ripe Tomato	0.86579	0.224
Mature Eggplant/Ripe Tomato	6.50718	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0412	1
1-1-2/M82	1.03483	1
12-2/M82	N/A	N/A
12-4/M82	1.71798	0.694
1-3/M82	0.76699	0.378
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.97749	1
3-2/M82	0.89553
4-1-1/M82	0.69936
4-1/M82	0.89935	1
4-3-2/M82	1.63755	0.508
4-3/M82	N/A	N/A
5-3/M82	1.00654	1
6-2/M82	N/A	N/A
6-3/M82	0.83995
7-1/M82	1.28912
7-2/M82	0.99275	1
9-3-2/M82	1.4732	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94326	1
IL2-6/WTpooled	0.7122	0.337
IL7-5/WTpooled	0.80014	1
IL7-3/WTpooled	1.02427	1
IL12-4/WTpooled	0.89801	0.71
IL1-4/WTpooled	1.04323	1
WT/WTpooled	1.04942	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	1.13116	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04381	0.921
DC3000/delta hrp 6h	1.01606	1
DC3000/delta hrp 12h	1.17619	1
DC3000/delta hrp 24h	0.48735	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67251	0.023
DC3000 delta B/DC3000 delta AB	0.64048	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89317	1
Exp 36h	0.95026	0.879
Exp 60h	0.77738	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02179	1
Var 0h	0.77997	0.933
Var 12h I row2-row1	1.07276	0.654
Var 12h NI row2-row1	1.03334	1
Var 36h I row2-row1	1.01556	1
Var 36h NI row2-row1	1.09635	0.482
Var 60h I row2-row1	0.66097	0.285
Var 60h NI row2-row1	1.09283	0.904
Time course 0hI-0hNI	1.08646	0.764
Time course 12hI-12hNI	1.07674	0.572
Time course 36hI-36hNI	1.16649	0.023
Time course 60hI-60hNI	1.4565	0.017

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)	0.93099	0.454
transgenic ySAMdc/azygous control (breaker)	1.46099	0.248
transgenic ySAMdc/azygous control (red)	0.9916	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8139	0.081

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64633	0.223

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.78284	0.096
Manapal/WT (break)	1.92396	0.126
Manapal/WT (red)	9.07768	0.164