Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.16.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08512	0.863
27DAP/17DAP	1.06883	0.91
39DAP/27DAP	1.15838	0.693
41DAP/39DAP	1.00296	0.967
42DAP/41DAP	0.83099	0.774
43DAP/42DAP	0.99791	0.937
47DAP/43DAP	0.97004	0.868
52DAP/47DAP	0.86235	0.619
57DAP/52DAP	0.93313	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89744	0.2
17DAP/reference	0.89171	0.065
27DAP/reference	1.08065	0.457
39DAP/reference	1.04458	0.504
41DAP/reference	0.93133	0.267
42DAP/reference	0.79251	0.001
43DAP/reference	0.99068	0.82
47DAP/reference	0.85976	0.027
52DAP/reference	0.91435	0.108
57DAP/reference	0.95049	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02157	1
27DAP/17DAP	0.99782	0.969
39DAP/27DAP	0.96458	0.804
41DAP/39DAP	1.05827	0.921
42DAP/41DAP	0.98551	0.77
43DAP/42DAP	1.0385	0.83
47DAP/43DAP	0.8288	0.195
52DAP/47DAP	1.06683	0.862
57DAP/52DAP	0.94433	0.608
57DAP/7DAP	1.44957	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9323	0.246
17DAP/reference	0.95114	0.22
27DAP/reference	0.92506	0.185
39DAP/reference	1.04138	0.819
41DAP/reference	0.92766	0.235
42DAP/reference	0.91835	0.275
43DAP/reference	0.9875	0.555
47DAP/reference	0.97529	0.671
52DAP/reference	0.91759	0.213
57DAP/reference	0.97113	0.494

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03897	0.943
17DAP/reference	0.91489	0.139
27DAP/reference	0.78916	0.045
39DAP/reference	0.83604	0.034
41DAP/reference	0.71002	0.108
42DAP/reference	0.78977	0.042
43DAP/reference	1.3145	0.219
47DAP/reference	0.92514	0.123
52DAP/reference	0.99227	0.619
57DAP/reference	0.99096	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99132	0.699
17DAP/reference	1.00888	0.855
27DAP/reference	0.95044	0.397
39DAP/reference	0.96316	0.464
41DAP/reference	1.00517	0.826
42DAP/reference	0.92881	0.445
43DAP/reference	1.00787	1
47DAP/reference	0.95944	0.383
52DAP/reference	0.85944	0.216
57DAP/reference	0.8841	0.107

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0418	0.966
26DAP/20DAP	1.11609	0.924
34DAP/26DAP	1.17471	1
51DAP/34DAP	1.04617	0.901
52DAP/51DAP	1.08725	0.848
53DAP/52DAP	1.03721	0.91
55DAP/53DAP	1.09195	0.922
57DAP/55DAP	1.0271	1
62DAP/57DAP	1.03697	1
68DAP/62DAP	0.77787	0.429
68DAP/14DAP	0.88144	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82306	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.12815	0.577
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.9566
Mature Eggplant/Ripe Tomato	1.51508	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01875	1
1-1-2/M82	0.82706	1
12-2/M82	1.01151	1
12-4/M82	0.96597	1
1-3/M82	0.68523	0.501
2-1-1/M82	0.91583	1
2-1/M82	N/A	N/A
2-6/M82	1.02895
3-2/M82	0.94395	1
4-1-1/M82	1.11475	1
4-1/M82	0.75409
4-3-2/M82	0.94027	1
4-3/M82	0.93741	0.578
5-3/M82	0.94446	0.642
6-2/M82	0.80632
6-3/M82	1.11264
7-1/M82	1.37464
7-2/M82	0.96353	0.881
9-3-2/M82	1.05011	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.17099	0.365
IL2-6/WTpooled	0.71711	0.473
IL7-5/WTpooled	0.97232	1
IL7-3/WTpooled	0.72502	0.31
IL12-4/WTpooled	1.12664	0.785
IL1-4/WTpooled	1.09391	1
WT/WTpooled	0.95671	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	0.80185

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.945	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.01923	1
DC3000/delta hrp 24h	1.11518	0.271

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.01178	1
Var 0h	0.98034	1
Var 12h I row2-row1	1.1386	0.443
Var 12h NI row2-row1	0.83183	0.546
Var 36h I row2-row1	0.7735	0.805
Var 36h NI row2-row1	0.61285	0.791
Var 60h I row2-row1	1.114	0.389
Var 60h NI row2-row1	2.04189	0.904
Time course 0hI-0hNI	1.1993	0.603
Time course 12hI-12hNI	1.15017	0.774
Time course 36hI-36hNI	0.98294	0.601
Time course 60hI-60hNI	0.76114	1

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)	1.28079	1
transgenic ySAMdc/azygous control (breaker)	2.89758	0.248
transgenic ySAMdc/azygous control (red)	1.57229	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01017	0.656

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35253	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81531	1
Manapal/WT (break)	0.98973	1
Manapal/WT (red)	0.93898	0.424