Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.15.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99362	0.876
27DAP/17DAP	1.0025	1
39DAP/27DAP	0.93602	0.641
41DAP/39DAP	1.35369	0.323
42DAP/41DAP	1.00592	1
43DAP/42DAP	0.94489	0.801
47DAP/43DAP	0.98091	0.89
52DAP/47DAP	1.10389	0.787
57DAP/52DAP	0.99117	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97677	0.489
17DAP/reference	0.99853	1
27DAP/reference	0.99277	0.779
39DAP/reference	0.96409	0.554
41DAP/reference	0.88516	0.026
42DAP/reference	0.96089	0.043
43DAP/reference	0.94838	0.316
47DAP/reference	0.97815	0.345
52DAP/reference	1.01335	1
57DAP/reference	0.96638	0.358

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94374	0.496
27DAP/17DAP	0.94151	0.475
39DAP/27DAP	1.01296	0.799
41DAP/39DAP	1.00228	1
42DAP/41DAP	0.94939	0.568
43DAP/42DAP	0.99524	1
47DAP/43DAP	1.03332	0.848
52DAP/47DAP	0.9942	0.959
57DAP/52DAP	1.01495	0.992
57DAP/7DAP	0.97769	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9543	0.146
17DAP/reference	0.94191	0.056
27DAP/reference	0.94075	0.033
39DAP/reference	0.959	0.083
41DAP/reference	1.00355	1
42DAP/reference	0.97557	0.222
43DAP/reference	0.98065	0.527
47DAP/reference	0.92494	0.079
52DAP/reference	0.973	0.363
57DAP/reference	0.92121	0.056

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9765	0.592
17DAP/reference	0.91262	0.113
27DAP/reference	1.03987	0.692
39DAP/reference	1.0025	0.769
41DAP/reference	0.97556	0.432
42DAP/reference	1.02611	1
43DAP/reference	0.99825	0.814
47DAP/reference	0.91644	0.12
52DAP/reference	0.97924	0.5
57DAP/reference	0.96584	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98319	0.135
17DAP/reference	0.95316	0.239
27DAP/reference	0.9377	0.028
39DAP/reference	0.93214	0.076
41DAP/reference	0.96606	0.264
42DAP/reference	0.97666	0.671
43DAP/reference	0.93803	0.12
47DAP/reference	0.96259	0.259
52DAP/reference	0.90457	0.204
57DAP/reference	1.01985	0.971

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.98283	1
26DAP/20DAP	1.01232	1
34DAP/26DAP	0.97652	0.961
51DAP/34DAP	1.06309	0.73
52DAP/51DAP	1.06504	0.503
53DAP/52DAP	0.93128	0.767
55DAP/53DAP	0.99743	0.864
57DAP/55DAP	1.3195	0.779
62DAP/57DAP	0.99624	0.994
68DAP/62DAP	0.93884	0.406
68DAP/14DAP	1.4473	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.00022	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.76834	0.245
Mature Green Tomato/Ripe Tomato	0.85681	0.165
Immature Eggplant/Mature Eggplant	1.02803	1
Ripe Pepper/Ripe Tomato	1.81963	1
Mature Eggplant/Ripe Tomato	1.64114	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99746	1
1-1-2/M82	0.98481	1
12-2/M82	0.98373	1
12-4/M82	0.98282	1
1-3/M82	0.98043	0.501
2-1-1/M82	0.92727	0.465
2-1/M82	1.15739
2-6/M82	0.96006	1
3-2/M82	1.00335	1
4-1-1/M82	1.0521	1
4-1/M82	0.99785	1
4-3-2/M82	1.01951	1
4-3/M82	0.94236	0.72
5-3/M82	1.03748	1
6-2/M82	1.01684	1
6-3/M82	0.99077	1
7-1/M82	0.90219	0.452
7-2/M82	0.96091	0.796
9-3-2/M82	0.88677	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.12502	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.86375	0.298
IL12-4/WTpooled	1.00816	1
IL1-4/WTpooled	0.95	0.834
WT/WTpooled	1.06594	0.87

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	1.34277	0.075

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93114	0.941
DC3000/delta hrp 6h	0.93368	0.95
DC3000/delta hrp 12h	0.94814	1
DC3000/delta hrp 24h	0.979	0.91

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06934	0.11
DC3000 delta B/DC3000 delta AB	0.99398	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07869	1
Exp 36h	1.35677	0.489
Exp 60h	1.34615	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97932	1
Var 0h	0.33116	0.457
Var 12h I row2-row1	1.11212	0.379
Var 12h NI row2-row1	1.0608	1
Var 36h I row2-row1	0.9606	1
Var 36h NI row2-row1	0.99629	1
Var 60h I row2-row1	1.05125	0.543
Var 60h NI row2-row1	1.0272	1
Time course 0hI-0hNI	1.00149	1
Time course 12hI-12hNI	1.06974	0.55
Time course 36hI-36hNI	1.0096	0.975
Time course 60hI-60hNI	1.63862	0.015

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)	1.11583	0.339
transgenic ySAMdc/azygous control (breaker)	0.83045	0.129
transgenic ySAMdc/azygous control (red)	1.11174	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01328	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98582	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98507	1
Manapal/WT (break)	0.79405	0.333
Manapal/WT (red)	0.76633	0.183