Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.6.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.45369	0.211
27DAP/17DAP	1.37194	0.683
39DAP/27DAP	0.80634	0.392
41DAP/39DAP	1.06783	0.696
42DAP/41DAP	1.05365	0.949
43DAP/42DAP	1.11764	0.982
47DAP/43DAP	1.23894	0.576
52DAP/47DAP	0.71911	0.35
57DAP/52DAP	1.09279	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99776	0.787
17DAP/reference	1.06877	0.092
27DAP/reference	1.02891	0.648
39DAP/reference	0.99562	0.941
41DAP/reference	1.03244	0.624
42DAP/reference	0.96746	0.072
43DAP/reference	1.0201	0.758
47DAP/reference	1.01747	0.728
52DAP/reference	0.94752	0.25
57DAP/reference	1.01842	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.14957	0.036
27DAP/17DAP	0.83296	0.312
39DAP/27DAP	1.17782	0.182
41DAP/39DAP	0.99517	1
42DAP/41DAP	1.054	0.924
43DAP/42DAP	1.94902	0.013
47DAP/43DAP	1.03139	0.941
52DAP/47DAP	0.85809	0.076
57DAP/52DAP	0.65274	0.123
57DAP/7DAP	1.22863	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97194	0.402
17DAP/reference	0.81464	0.035
27DAP/reference	0.82273	0.01
39DAP/reference	1.48669	0.006
41DAP/reference	0.93335	0.107
42DAP/reference	1.37056	0.03
43DAP/reference	2.07349	0.007
47DAP/reference	1.50591	0.337
52DAP/reference	2.05318	0.007
57DAP/reference	1.96571	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97463	0.532
17DAP/reference	1.04996	0.348
27DAP/reference	0.93304	0.229
39DAP/reference	0.96642	0.404
41DAP/reference	0.95039	0.194
42DAP/reference	0.9617	0.289
43DAP/reference	0.97163	0.561
47DAP/reference	0.95964	0.253
52DAP/reference	0.991	0.619
57DAP/reference	1.08243	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80008	0.041
17DAP/reference	1.00244	0.886
27DAP/reference	0.89153	0.097
39DAP/reference	0.86958	0.043
41DAP/reference	0.99542	0.754
42DAP/reference	0.97443	0.671
43DAP/reference	1.24871	0.241
47DAP/reference	0.95282	0.396
52DAP/reference	1.05382	0.862
57DAP/reference	0.80303	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01657	0.966
26DAP/20DAP	1.6252	0.103
34DAP/26DAP	1.08623	1
51DAP/34DAP	0.85555	0.274
52DAP/51DAP	0.80954	0.151
53DAP/52DAP	1.15	0.356
55DAP/53DAP	0.79676	0.033
57DAP/55DAP	0.84865	0.423
62DAP/57DAP	1.01233	1
68DAP/62DAP	1.16836	0.788
68DAP/14DAP	1.08767	0.541

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91246	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.20961	0.075
Mature Green Tomato/Ripe Tomato	0.88067	0.256
Immature Eggplant/Mature Eggplant	1.21023	0.321
Ripe Pepper/Ripe Tomato	1.70127	1
Mature Eggplant/Ripe Tomato	2.56808	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02043	1
1-1-2/M82	0.84166
12-2/M82	0.86822	0.955
12-4/M82	0.88778	1
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	1.30016
3-2/M82	1.14948
4-1-1/M82	N/A	N/A
4-1/M82	1.13944
4-3-2/M82	1.65607	1
4-3/M82	1.45343	1
5-3/M82	1.06714	0.436
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.86018
7-2/M82	N/A	N/A
9-3-2/M82	0.84014	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.06324	1
IL7-5/WTpooled	1.01393
IL7-3/WTpooled	1.28258	1
IL12-4/WTpooled	0.78132	0.543
IL1-4/WTpooled	1.22635	0.426
WT/WTpooled	0.9084	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	0.99129	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95213	1
DC3000/delta hrp 6h	0.96494	0.95
DC3000/delta hrp 12h	1.02173	1
DC3000/delta hrp 24h	0.74319	0.114

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.89898	0.803
DC3000 delta B/DC3000 delta AB	1.0716	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.75271	1
Exp 36h	0.9397	0.943
Exp 60h	0.65224	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03916	1
Var 0h	0.80842	0.933
Var 12h I row2-row1	1.01744	1
Var 12h NI row2-row1	1.10145	0.649
Var 36h I row2-row1	1.24322	0.304
Var 36h NI row2-row1	1.11928	1
Var 60h I row2-row1	0.87534	0.582
Var 60h NI row2-row1	0.93313	1
Time course 0hI-0hNI	1.11586	0.377
Time course 12hI-12hNI	0.95348	0.698
Time course 36hI-36hNI	0.88786	0.206
Time course 60hI-60hNI	1.02025	0.495

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)	0.95943	0.428
transgenic ySAMdc/azygous control (breaker)	1.48508	0.248
transgenic ySAMdc/azygous control (red)	1.11768	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93336	0.06

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.62782	0.172
Manapal/WT (break)	0.93062	1
Manapal/WT (red)	0.70153	0.229