Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.3.6

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80856	0.318
27DAP/17DAP	0.80642	0.5
39DAP/27DAP	1.03605	0.857
41DAP/39DAP	1.15947	0.53
42DAP/41DAP	1.07631	0.913
43DAP/42DAP	1.0652	1
47DAP/43DAP	0.96108	0.821
52DAP/47DAP	1.0422	0.915
57DAP/52DAP	0.94057	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02869	0.96
17DAP/reference	0.6273	0.007
27DAP/reference	0.74155	0.07
39DAP/reference	0.79386	0.013
41DAP/reference	0.64122	0.009
42DAP/reference	0.95273	0.337
43DAP/reference	0.74256
47DAP/reference	1.13681	0.524
52DAP/reference	1.92882	0.017
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24032	0.083
27DAP/17DAP	1.17458	0.37
39DAP/27DAP	0.97427	0.833
41DAP/39DAP	0.95454	0.875
42DAP/41DAP	1.21181	0.208
43DAP/42DAP	0.91963	0.482
47DAP/43DAP	1.0819	0.772
52DAP/47DAP	1.09083	0.718
57DAP/52DAP	1.0593	0.783
57DAP/7DAP	1.19079	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14512	0.6
17DAP/reference	0.94	0.167
27DAP/reference	1.12955	0.197
39DAP/reference	0.97735	0.474
41DAP/reference	1.04179	0.836
42DAP/reference	1.34487	0.174
43DAP/reference	1.25614	0.048
47DAP/reference	1.7983	0.014
52DAP/reference	1.36736	0.019
57DAP/reference	1.13198	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04863	0.93
17DAP/reference	0.65807	0.024
27DAP/reference	1.45642	0.217
39DAP/reference	1.18955	0.806
41DAP/reference	1.14964	0.657
42DAP/reference	1.35484	0.041
43DAP/reference	0.91137	0.336
47DAP/reference	1.18775	0.413
52DAP/reference	0.72476	0.003
57DAP/reference	0.56567	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09481	0.793
17DAP/reference	0.8865	0.389
27DAP/reference	1.12624	0.085
39DAP/reference	1.35595	0.024
41DAP/reference	0.97786	0.459
42DAP/reference	1.4365	0.06
43DAP/reference	1.66852	0.087
47DAP/reference	0.77572	0.049
52DAP/reference	1.3697	0.153
57DAP/reference	3.44397	0.006

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	2.97513	1
26DAP/20DAP	1.30179	0.437
34DAP/26DAP	0.84485	0.121
51DAP/34DAP	2.33668	0.025
52DAP/51DAP	0.93342	1
53DAP/52DAP	1.31879	0.274
55DAP/53DAP	0.74443	0.149
57DAP/55DAP	0.72296	0.096
62DAP/57DAP	0.71664	0.002
68DAP/62DAP	1.48871	0.316
68DAP/14DAP	2.33135	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.26988	0.306

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85429	0.323
Mature Green Tomato/Ripe Tomato	1.36584	0.064
Immature Eggplant/Mature Eggplant	1.87805	0.05
Ripe Pepper/Ripe Tomato	1.15987	1
Mature Eggplant/Ripe Tomato	0.70659	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92777
1-1-2/M82	1.89253
12-2/M82	1.19203	1
12-4/M82	0.92831	1
1-3/M82	2.31935	0.255
2-1-1/M82	0.78342	0.465
2-1/M82	N/A	N/A
2-6/M82	0.77857	1
3-2/M82	N/A	N/A
4-1-1/M82	0.67259	1
4-1/M82	0.52985
4-3-2/M82	0.98725	1
4-3/M82	1.13329	0.268
5-3/M82	1.18353	0.572
6-2/M82	1.00953
6-3/M82	0.86319	1
7-1/M82	N/A	N/A
7-2/M82	1.32977
9-3-2/M82	0.81651	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95678	1
IL2-6/WTpooled	0.72797	0.383
IL7-5/WTpooled	0.77858
IL7-3/WTpooled	1.08475	1
IL12-4/WTpooled	1.04097	0.839
IL1-4/WTpooled	0.94841	1
WT/WTpooled	1.06641	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	1.10028	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01461	0.921
DC3000/delta hrp 6h	0.96351	0.95
DC3000/delta hrp 12h	1.02887	1
DC3000/delta hrp 24h	0.75835	0.087

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34793
DC3000 delta B/DC3000 delta AB	1.3273	0.151

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12432	1
Exp 36h	1.44024	0.693
Exp 60h	1.45256	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99041	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.9778
Var 12h NI row2-row1	0.97105
Var 36h I row2-row1	1.21446	0.309
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	0.97208	0.903
Time course 12hI-12hNI	1.10207	0.327
Time course 36hI-36hNI	1.15049	0.056
Time course 60hI-60hNI	1.74284	0.009

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)	0.80445	0.314
transgenic ySAMdc/azygous control (breaker)	0.66134	0.142
transgenic ySAMdc/azygous control (red)	0.94686	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14743	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72981	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05613	1
Manapal/WT (break)	1.36605	0.183
Manapal/WT (red)	1.03307	1