Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.5.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03284	0.977
27DAP/17DAP	1.20682	0.825
39DAP/27DAP	0.88502	0.325
41DAP/39DAP	0.99026	0.944
42DAP/41DAP	0.86565	1
43DAP/42DAP	1.13967	0.861
47DAP/43DAP	1.01197	0.943
52DAP/47DAP	0.76407	0.381
57DAP/52DAP	1.12315	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44992	0.105
17DAP/reference	1.40202	0.086
27DAP/reference	1.02949	0.885
39DAP/reference	0.91636	0.391
41DAP/reference	1.33227	0.019
42DAP/reference	1.32533	0.21
43DAP/reference	1.1592	0.175
47DAP/reference	0.9634	0.392
52DAP/reference	0.82527	0.069
57DAP/reference	0.79764	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03731	0.774
27DAP/17DAP	1.07607	0.951
39DAP/27DAP	0.86593	0.04
41DAP/39DAP	1.11338	0.663
42DAP/41DAP	0.99608	0.887
43DAP/42DAP	1.03555	0.413
47DAP/43DAP	0.99504	0.99
52DAP/47DAP	0.91006	0.645
57DAP/52DAP	0.92603	0.555
57DAP/7DAP	0.67371	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	0.94707	0.124
27DAP/reference	0.96597	0.094
39DAP/reference	0.90048	0.02
41DAP/reference	0.97932	0.235
42DAP/reference	0.9898	0.612
43DAP/reference	0.95741	0.334
47DAP/reference	0.7358	0.383
52DAP/reference	0.85881	0.016
57DAP/reference	0.9189	0.097

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.78553	0.039
17DAP/reference	1.15376	0.531
27DAP/reference	1.19634	1
39DAP/reference	0.92854	0.348
41DAP/reference	1.16325	0.277
42DAP/reference	0.82908	0.189
43DAP/reference	1.10958	1
47DAP/reference	1.11496	0.377
52DAP/reference	1.09749	0.471
57DAP/reference	0.9533	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0239	0.723
17DAP/reference	1.10499	0.65
27DAP/reference	N/A	N/A
39DAP/reference	1.00509	0.962
41DAP/reference	1.6055	0.621
42DAP/reference	1.19284	0.635
43DAP/reference	0.93842	0.614
47DAP/reference	0.97773	0.538
52DAP/reference	0.94179	0.482
57DAP/reference	0.72914	0.208

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01982	1
26DAP/20DAP	1.00595	1
34DAP/26DAP	1.05635	1
51DAP/34DAP	1.04441	0.909
52DAP/51DAP	1.0185	0.888
53DAP/52DAP	1.05771	0.806
55DAP/53DAP	0.93823	0.709
57DAP/55DAP	1.10008	0.969
62DAP/57DAP	1.45116	0.622
68DAP/62DAP	0.61948	0.152
68DAP/14DAP	0.85461

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87693	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.16828	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	7.49841

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96035	0.944
1-1-2/M82	0.94254	1
12-2/M82	N/A	N/A
12-4/M82	0.87321	1
1-3/M82	N/A	N/A
2-1-1/M82	0.72798
2-1/M82	N/A	N/A
2-6/M82	1.27631	0.505
3-2/M82	1.08138
4-1-1/M82	1.32525
4-1/M82	0.82268	0.665
4-3-2/M82	0.88158	1
4-3/M82	N/A	N/A
5-3/M82	0.90834	0.642
6-2/M82	1.19787
6-3/M82	N/A	N/A
7-1/M82	0.92646
7-2/M82	1.03038
9-3-2/M82	0.92753	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85833	0.321
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	0.855	0.559
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.00215	1
WT/WTpooled	1.50867

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	0.87881	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07586	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.22891	1
DC3000/delta hrp 24h	0.33544	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55891	0.025
DC3000 delta B/DC3000 delta AB	0.57099	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0725	1
Var 0h	0.54225	1
Var 12h I row2-row1	0.92051	0.418
Var 12h NI row2-row1	1.00539	1
Var 36h I row2-row1	0.93524	0.374
Var 36h NI row2-row1	1.24659	0.482
Var 60h I row2-row1	0.98662	0.952
Var 60h NI row2-row1	1.13881	0.904
Time course 0hI-0hNI	0.9725	0.861
Time course 12hI-12hNI	1.08243	0.213
Time course 36hI-36hNI	0.97893	0.589
Time course 60hI-60hNI	0.31055	0.006

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.60265	1
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.06711	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.40613	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.00701	1
Manapal/WT (red)	2.5139	0.15