Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11686	0.827
27DAP/17DAP	1.03631	1
39DAP/27DAP	1.01205	0.84
41DAP/39DAP	1.05707	0.914
42DAP/41DAP	1.09913	0.913
43DAP/42DAP	1.19046	0.823
47DAP/43DAP	1.098	0.448
52DAP/47DAP	0.8614	0.623
57DAP/52DAP	0.87675	0.839

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89319	0.154
17DAP/reference	1.03019	0.399
27DAP/reference	0.97952	0.654
39DAP/reference	0.93409	0.381
41DAP/reference	0.82712	0.009
42DAP/reference	1.09829	0.027
43DAP/reference	0.976	0.691
47DAP/reference	0.98331	0.503
52DAP/reference	1.14103	0.205
57DAP/reference	1.02841	0.682

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.18479	0.158
27DAP/17DAP	0.86906	0.206
39DAP/27DAP	0.83027	0.126
41DAP/39DAP	0.92873	0.747
42DAP/41DAP	0.89697	0.303
43DAP/42DAP	1.19289	0.25
47DAP/43DAP	0.93277	0.617
52DAP/47DAP	0.95014	0.66
57DAP/52DAP	1.20699	0.344
57DAP/7DAP	0.87319	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92795	0.138
17DAP/reference	1.02668	1
27DAP/reference	0.87231	0.03
39DAP/reference	0.83776	0.014
41DAP/reference	0.95842	0.412
42DAP/reference	1.00466	0.713
43DAP/reference	1.13865	0.06
47DAP/reference	0.92179	0.383
52DAP/reference	1.00409	0.74
57DAP/reference	1.69605	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82408	0.033
17DAP/reference	0.75378	0.047
27DAP/reference	0.96508	0.452
39DAP/reference	0.90402	0.095
41DAP/reference	1.20801	0.027
42DAP/reference	0.90811	0.237
43DAP/reference	0.92895	0.352
47DAP/reference	0.98128	0.512
52DAP/reference	0.83476	0.004
57DAP/reference	0.86029	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78568	0.038
17DAP/reference	0.93589	0.47
27DAP/reference	1.1957	0.092
39DAP/reference	1.00904	0.987
41DAP/reference	0.9731	0.56
42DAP/reference	0.91512	0.22
43DAP/reference	1.12326	0.223
47DAP/reference	1.02108	1
52DAP/reference	1.37521	0.141
57DAP/reference	1.26819	0.324

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26858	0.966
26DAP/20DAP	0.64712	0.317
34DAP/26DAP	0.96345	0.961
51DAP/34DAP	1.28462	0.314
52DAP/51DAP	0.83918	1
53DAP/52DAP	0.82895	0.316
55DAP/53DAP	1.10301	0.876
57DAP/55DAP	0.88253	0.521
62DAP/57DAP	1.18785	0.833
68DAP/62DAP	1.49931	0.153
68DAP/14DAP	2.89933	0.039

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8245	0.166

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.33889	0.073
Mature Green Tomato/Ripe Tomato	1.14611	0.632
Immature Eggplant/Mature Eggplant	1.08729	0.379
Ripe Pepper/Ripe Tomato	0.48037	0.224
Mature Eggplant/Ripe Tomato	0.29076

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.99866	1
1-3/M82	0.81412	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.19086
3-2/M82	1.77987
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.81131
4-3/M82	N/A	N/A
5-3/M82	0.87668
6-2/M82	1.31309
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.99891

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.9312	1
IL2-6/WTpooled	1.0765	0.659
IL7-5/WTpooled	2.01774
IL7-3/WTpooled	0.84965	0.418
IL12-4/WTpooled	1.09477	0.839
IL1-4/WTpooled	0.96305	1
WT/WTpooled	0.92133	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	0.92066	0.341

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84321	1
DC3000/delta hrp 6h	1.13019	0.392
DC3000/delta hrp 12h	1.17035	1
DC3000/delta hrp 24h	0.55928	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.71409	0.388
DC3000 delta B/DC3000 delta AB	0.59904	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02395	1
Exp 36h	1.32156	0.489
Exp 60h	1.43995	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98852	1
Var 0h	0.55005	0.936
Var 12h I row2-row1	0.87739	0.514
Var 12h NI row2-row1	0.9646	0.82
Var 36h I row2-row1	1.10806	0.908
Var 36h NI row2-row1	1.20996	0.253
Var 60h I row2-row1	1.08021	0.562
Var 60h NI row2-row1	1.21969	0.904
Time course 0hI-0hNI	1.01802	1
Time course 12hI-12hNI	0.95145	0.562
Time course 36hI-36hNI	0.84856	0.112
Time course 60hI-60hNI	0.21808	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)	1.20677	0.455
transgenic ySAMdc/azygous control (breaker)	0.63336	0.15
transgenic ySAMdc/azygous control (red)	1.00215	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04796	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.15581	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69157	0.172
Manapal/WT (break)	0.96713	1
Manapal/WT (red)	1.27872	1