Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.20.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95309	0.652
27DAP/17DAP	1.19807	0.842
39DAP/27DAP	0.81096	0.449
41DAP/39DAP	1.62678	0.37
42DAP/41DAP	0.97698	1
43DAP/42DAP	1.16701	0.823
47DAP/43DAP	1.11676	0.873
52DAP/47DAP	1.00772	0.906
57DAP/52DAP	0.86719	0.756

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92685	0.159
17DAP/reference	1.07362	0.178
27DAP/reference	1.03946	0.446
39DAP/reference	1.05551	0.359
41DAP/reference	0.96774	0.667
42DAP/reference	0.90413	0.022
43DAP/reference	0.98392	0.745
47DAP/reference	0.93632	0.148
52DAP/reference	0.92502	0.21
57DAP/reference	0.86767	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17031	0.975
27DAP/17DAP	1.23754	0.912
39DAP/27DAP	1.27514	0.596
41DAP/39DAP	1.20409	0.88
42DAP/41DAP	0.91713	0.503
43DAP/42DAP	0.92977	0.597
47DAP/43DAP	0.71955	0.339
52DAP/47DAP	0.93687	0.797
57DAP/52DAP	1.38398	0.497
57DAP/7DAP	2.02681	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03763	1
17DAP/reference	0.91889	0.338
27DAP/reference	1.01664	1
39DAP/reference	0.65701	0.02
41DAP/reference	0.73401	0.039
42DAP/reference	0.72	0.012
43DAP/reference	0.72505	0.028
47DAP/reference	0.8187	0.168
52DAP/reference	0.78465	0.066
57DAP/reference	0.62391	0.071

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93283	0.399
17DAP/reference	0.96178	0.422
27DAP/reference	0.87088	0.087
39DAP/reference	0.81025	0.02
41DAP/reference	0.8284	0.021
42DAP/reference	0.6418	0.011
43DAP/reference	0.97526	0.581
47DAP/reference	0.94533	0.379
52DAP/reference	1.04146	0.596
57DAP/reference	1.00729	0.916

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88275	0.214
17DAP/reference	0.90625	0.249
27DAP/reference	0.85609	0.155
39DAP/reference	0.92724	0.299
41DAP/reference	0.95913	0.417
42DAP/reference	0.88957	0.287
43DAP/reference	0.9738	0.568
47DAP/reference	0.93404	0.286
52DAP/reference	2.04259	0.216
57DAP/reference	0.78366	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00379	1
26DAP/20DAP	0.65669	0.228
34DAP/26DAP	1.18101	1
51DAP/34DAP	1.06113	0.949
52DAP/51DAP	1.19654	0.099
53DAP/52DAP	1.08067	0.848
55DAP/53DAP	0.80775	0.515
57DAP/55DAP	1.31023	0.898
62DAP/57DAP	1.1469	0.935
68DAP/62DAP	1.28329	0.95
68DAP/14DAP	0.87889	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.12351

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.96128	0.551
Mature Green Tomato/Ripe Tomato	1.01222	0.898
Immature Eggplant/Mature Eggplant	1.217	0.334
Ripe Pepper/Ripe Tomato	1.54324
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.9109
12-2/M82	N/A	N/A
12-4/M82	0.5389
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
4-1/M82	0.7821	0.737
4-3-2/M82	0.8245
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.86464
7-2/M82	N/A	N/A
9-3-2/M82	0.73907	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.20702	0.277
IL2-6/WTpooled	0.91661	1
IL7-5/WTpooled	1.21841	0.75
IL7-3/WTpooled	1.26035	1
IL12-4/WTpooled	1.04579	0.516
IL1-4/WTpooled	1.08588	0.426
WT/WTpooled	0.99056	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	1.0384

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	0.94744	0.95
DC3000/delta hrp 12h	0.99135	1
DC3000/delta hrp 24h	1.4391

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	0.99192	1
Exp 36h	0.83389	0.419
Exp 60h	0.86214	0.343

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

hybridization	ratio	FDR (corrected p value)
self-self	0.64154
Var 0h	N/A	N/A
Var 12h I row2-row1	6.53767	0.473
Var 12h NI row2-row1	1.15542	1
Var 36h I row2-row1	0.90746
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.647
Var 60h NI row2-row1	0.67087	1
Time course 0hI-0hNI	1.16194	0.867
Time course 12hI-12hNI	0.89829	0.719
Time course 36hI-36hNI	1.50477	0.166
Time course 60hI-60hNI	1.1944	1

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)	0.93713	0.32
transgenic ySAMdc/azygous control (breaker)	1.0585	1
transgenic ySAMdc/azygous control (red)	1.03704	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05256	0.059

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0083	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.93993	1
Manapal/WT (break)	0.99702	1
Manapal/WT (red)	1.2709	0.413