Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72815	0.166
27DAP/17DAP	0.80654	0.539
39DAP/27DAP	1.10918	0.922
41DAP/39DAP	0.95849	0.791
42DAP/41DAP	0.85654	1
43DAP/42DAP	1.33949	0.499
47DAP/43DAP	0.79399	0.402
52DAP/47DAP	0.99777	0.942
57DAP/52DAP	1.54952	0.843

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21527	0.028
17DAP/reference	0.80425	0.015
27DAP/reference	0.99917	0.779
39DAP/reference	0.83872	0.047
41DAP/reference	0.81838	0.267
42DAP/reference	0.89838	0.062
43DAP/reference	1.01368	0.924
47DAP/reference	0.87495	0.065
52DAP/reference	0.93325	0.237
57DAP/reference	1.03818	0.643

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02781	1
27DAP/17DAP	1.06754	0.842
39DAP/27DAP	0.7498	0.041
41DAP/39DAP	1.00097	1
42DAP/41DAP	1.07265	0.763
43DAP/42DAP	0.97687	0.641
47DAP/43DAP	1.06215	0.844
52DAP/47DAP	0.95778	0.857
57DAP/52DAP	0.98279	0.793
57DAP/7DAP	0.63624	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.06179	0.03
17DAP/reference	3.47515	0.006
27DAP/reference	3.5681	0.006
39DAP/reference	3.19509	0.005
41DAP/reference	2.49782	0.113
42DAP/reference	3.94399	0.007
43DAP/reference	4.58476	0.007
47DAP/reference	2.96608	0.161
52DAP/reference	4.05913	0.007
57DAP/reference	3.46343	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02612	0.874
17DAP/reference	0.88637	0.106
27DAP/reference	0.91509	0.249
39DAP/reference	0.79987	0.122
41DAP/reference	0.87062	0.148
42DAP/reference	0.88964	0.212
43DAP/reference	0.68771	0.04
47DAP/reference	0.85991	0.05
52DAP/reference	0.84429	0.072
57DAP/reference	0.64303	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.64864	0.022
17DAP/reference	1.83991	0.45
27DAP/reference	4.49853	0.034
39DAP/reference	4.69732	0.067
41DAP/reference	2.77117	0.026
42DAP/reference	2.51394	0.18
43DAP/reference	3.41447	0.056
47DAP/reference	1.02076	1
52DAP/reference	3.29378	0.155
57DAP/reference	1.14631	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.36712	0.945
26DAP/20DAP	1.3324	0.555
34DAP/26DAP	1.08805	1
51DAP/34DAP	1.36505	0.046
52DAP/51DAP	1.3273	0.041
53DAP/52DAP	0.84901	0.183
55DAP/53DAP	0.75685	0.05
57DAP/55DAP	1.07039	0.947
62DAP/57DAP	0.96339	0.994
68DAP/62DAP	1.39756	0.054
68DAP/14DAP	1.34028	0.084

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.313	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71208	0.207
Mature Green Tomato/Ripe Tomato	2.41552	0.209
Immature Eggplant/Mature Eggplant	0.59863	0.058
Ripe Pepper/Ripe Tomato	2.31284	0.258
Mature Eggplant/Ripe Tomato	3.62645	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.57321
1-1-2/M82	1.03087	1
12-2/M82	0.84385	0.56
12-4/M82	0.74281	1
1-3/M82	N/A	N/A
2-1-1/M82	0.82095	0.784
2-1/M82	0.76683	0.74
2-6/M82	1.1969
3-2/M82	N/A	N/A
4-1-1/M82	1.1443
4-1/M82	N/A	N/A
4-3-2/M82	1.23979
4-3/M82	1.78325	0.268
5-3/M82	1.00695	1
6-2/M82	N/A	N/A
6-3/M82	1.0721	1
7-1/M82	N/A	N/A
7-2/M82	1.13223
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06396	0.365
IL2-6/WTpooled	1.0462	0.659
IL7-5/WTpooled	0.90169	1
IL7-3/WTpooled	1.30695	1
IL12-4/WTpooled	0.93386	0.543
IL1-4/WTpooled	0.9103	0.834
WT/WTpooled	0.97837	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	0.90923	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96461	1
DC3000/delta hrp 6h	1.06378	1
DC3000/delta hrp 12h	0.89168	1
DC3000/delta hrp 24h	0.51231	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53765	0.024
DC3000 delta B/DC3000 delta AB	0.51546	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90018	1
Exp 36h	0.83624	0.661
Exp 60h	0.71193	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04235	1
Var 0h	1.09091	0.936
Var 12h I row2-row1	0.91026	0.627
Var 12h NI row2-row1	0.98319	0.713
Var 36h I row2-row1	0.94505	1
Var 36h NI row2-row1	1.26504	0.482
Var 60h I row2-row1	0.95172	0.439
Var 60h NI row2-row1	1.24878	0.904
Time course 0hI-0hNI	0.92847	0.461
Time course 12hI-12hNI	1.06347	0.507
Time course 36hI-36hNI	0.94679	0.403
Time course 60hI-60hNI	0.17149	0.005

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)	1.12721	0.339
transgenic ySAMdc/azygous control (breaker)	1.5547	0.162
transgenic ySAMdc/azygous control (red)	1.10821	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04472	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.61959	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.22643	0.083
Manapal/WT (break)	4.3496	0.123
Manapal/WT (red)	3.23819	0.15