Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.20.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92457	0.683
27DAP/17DAP	1.07208	0.9
39DAP/27DAP	1.38486	0.825
41DAP/39DAP	1.30249
42DAP/41DAP	0.72155	0.397
43DAP/42DAP	0.85181	0.776
47DAP/43DAP	1.12928	0.444
52DAP/47DAP	1.07501	0.898
57DAP/52DAP	0.86177	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89487	0.128
17DAP/reference	0.85568	0.046
27DAP/reference	1.08833	0.446
39DAP/reference	1.0463	0.615
41DAP/reference	0.89549	0.065
42DAP/reference	0.94012	0.124
43DAP/reference	0.91135	0.234
47DAP/reference	0.98546	0.503
52DAP/reference	1.01778	0.768
57DAP/reference	1.18904	0.035

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.46495	0.135
27DAP/17DAP	1.07893	0.798
39DAP/27DAP	1.01064	0.984
41DAP/39DAP	0.97123	0.945
42DAP/41DAP	1.23431	0.436
43DAP/42DAP	1.06993	0.446
47DAP/43DAP	1.06421	0.857
52DAP/47DAP	1.07143	0.819
57DAP/52DAP	1.28507	0.382
57DAP/7DAP	1.21282	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01866	1
17DAP/reference	0.89385	0.094
27DAP/reference	1.02794	0.804
39DAP/reference	0.81225	0.049
41DAP/reference	0.922	0.194
42DAP/reference	0.69983	0.01
43DAP/reference	0.81885	0.059
47DAP/reference	0.9994	1
52DAP/reference	1.07421	0.599
57DAP/reference	1.30038	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8993	0.222
17DAP/reference	0.90383	0.072
27DAP/reference	0.96503	0.452
39DAP/reference	0.96455	0.392
41DAP/reference	1.05532	1
42DAP/reference	0.94356	0.321
43DAP/reference	1.00892	0.801
47DAP/reference	0.92472	0.12
52DAP/reference	0.92181	0.156
57DAP/reference	0.90403	0.099

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8859	0.135
17DAP/reference	0.79901	0.132
27DAP/reference	0.89406	0.113
39DAP/reference	0.88294	0.063
41DAP/reference	0.92388	0.417
42DAP/reference	0.74713	0.108
43DAP/reference	0.86491	0.102
47DAP/reference	0.99562	0.646
52DAP/reference	1.15298	0.324
57DAP/reference	1.12128	0.332

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99097	1
26DAP/20DAP	1.17289	0.555
34DAP/26DAP	0.9061	0.753
51DAP/34DAP	1.17999	0.677
52DAP/51DAP	1.10086	0.776
53DAP/52DAP	1.07681	0.806
55DAP/53DAP	1.08503	0.982
57DAP/55DAP	1.14242	0.906
62DAP/57DAP	0.92338	0.871
68DAP/62DAP	1.6917	0.113
68DAP/14DAP	1.30757	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92815	0.399

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09862	0.176
Mature Green Tomato/Ripe Tomato	0.91514	0.522
Immature Eggplant/Mature Eggplant	1.1617	0.142
Ripe Pepper/Ripe Tomato	1.1465	1
Mature Eggplant/Ripe Tomato	0.94943	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.80154
1-1-2/M82	1.01991	1
12-2/M82	N/A	N/A
12-4/M82	1.05036	1
1-3/M82	0.94978
2-1-1/M82	0.99431	1
2-1/M82	0.80619
2-6/M82	0.8719	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.17919	0.512
4-3-2/M82	0.98174
4-3/M82	0.99803	1
5-3/M82	0.83505	0.642
6-2/M82	N/A	N/A
6-3/M82	0.99837
7-1/M82	0.55926	0.803
7-2/M82	0.80386	0.57
9-3-2/M82	0.93758	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93706	0.321
IL2-6/WTpooled	0.98216	1
IL7-5/WTpooled	0.84672	1
IL7-3/WTpooled	0.81648	1
IL12-4/WTpooled	0.92783	0.71
IL1-4/WTpooled	0.92768	0.699
WT/WTpooled	1.07738	0.818

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	1.0376	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04762	0.921
DC3000/delta hrp 6h	0.88053	0.95
DC3000/delta hrp 12h	0.9819	1
DC3000/delta hrp 24h	0.9562	0.861

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22643	0.313
DC3000 delta B/DC3000 delta AB	0.63621	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.82602	1
Exp 36h	1.01193	1
Exp 60h	0.9594	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	1.15296	0.296
Var 12h NI row2-row1	1.01847	1
Var 36h I row2-row1	0.97845	1
Var 36h NI row2-row1	0.76481	0.549
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.69352	0.932
Time course 0hI-0hNI	0.86025	0.415
Time course 12hI-12hNI	0.90458	0.464
Time course 36hI-36hNI	1.08664	0.355
Time course 60hI-60hNI	0.85197

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)	0.98461	0.567
transgenic ySAMdc/azygous control (breaker)	1.04356	1
transgenic ySAMdc/azygous control (red)	0.97191	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98369	0.371

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24415	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90751	1
Manapal/WT (break)	0.83015	0.333
Manapal/WT (red)	1.04457	0.222