Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.17.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96049	0.722
27DAP/17DAP	0.90388	0.779
39DAP/27DAP	0.95416	0.663
41DAP/39DAP	1.08588	0.962
42DAP/41DAP	1.0905	0.899
43DAP/42DAP	0.98682	0.925
47DAP/43DAP	0.72975	0.236
52DAP/47DAP	0.90728	0.702
57DAP/52DAP	1.31419	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08149	0.928
17DAP/reference	1.17508	0.201
27DAP/reference	0.84827	0.129
39DAP/reference	1.01934	1
41DAP/reference	1.40206	0.018
42DAP/reference	1.33424	0.001
43DAP/reference	1.16956	0.569
47DAP/reference	1.30577	0.007
52DAP/reference	1.23416	0.407
57DAP/reference	0.96491	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98004	0.663
27DAP/17DAP	0.87575	0.648
39DAP/27DAP	1.23945	0.171
41DAP/39DAP	1.30311	0.362
42DAP/41DAP	1.13018	0.753
43DAP/42DAP	1.25011	0.351
47DAP/43DAP	0.91174	0.63
52DAP/47DAP	1.08302	0.956
57DAP/52DAP	0.99776	0.81
57DAP/7DAP	0.7696	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48133	0.173
17DAP/reference	1.06987	1
27DAP/reference	0.91613	0.231
39DAP/reference	1.15255	0.391
41DAP/reference	1.36047	0.241
42DAP/reference	1.1717	0.686
43DAP/reference	1.01398	0.802
47DAP/reference	0.96042	0.504
52DAP/reference	0.88762	0.077
57DAP/reference	0.81903	0.034

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23883	0.874
17DAP/reference	0.91616	0.326
27DAP/reference	0.64467	0.167
39DAP/reference	1.06174	1
41DAP/reference	1.19008	0.513
42DAP/reference	1.50186	0.033
43DAP/reference	1.10877	0.793
47DAP/reference	1.16642	0.079
52DAP/reference	1.06297	1
57DAP/reference	0.99939	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98621	0.607
17DAP/reference	1.02611	0.934
27DAP/reference	0.97074	0.539
39DAP/reference	1.30601	0.285
41DAP/reference	1.08816	0.734
42DAP/reference	0.89696	0.287
43DAP/reference	1.00561	0.712
47DAP/reference	1.21656	0.792
52DAP/reference	1.34845	0.558
57DAP/reference	1.05248	0.933

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19701	1
26DAP/20DAP	0.95197	0.317
34DAP/26DAP	1.57538	0.542
51DAP/34DAP	1.25716	0.2
52DAP/51DAP	0.98481	1
53DAP/52DAP	0.78316	0.288
55DAP/53DAP	0.90758	0.273
57DAP/55DAP	1.25054	0.793
62DAP/57DAP	0.96486	0.994
68DAP/62DAP	0.62378	0.025
68DAP/14DAP	1.3838	0.521

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.94792	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.98983	0.835
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.07901
Mature Eggplant/Ripe Tomato	1.48483	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.88644
1-1-2/M82	1.11485	1
12-2/M82	1.15326
12-4/M82	1.00417
1-3/M82	1.13371
2-1-1/M82	1.18026
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.61636
4-1/M82	N/A	N/A
4-3-2/M82	0.84144
4-3/M82	1.05749
5-3/M82	0.99102	1
6-2/M82	N/A	N/A
6-3/M82	1.20508	1
7-1/M82	0.93629
7-2/M82	N/A	N/A
9-3-2/M82	1.02872

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.43558	1
IL12-4/WTpooled	1.20628	0.695
IL1-4/WTpooled	1.22352	0.426
WT/WTpooled	1.02871	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	0.8659	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.92672	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.30509	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95657
DC3000 delta B/DC3000 delta AB	0.72927	0.178

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	0.99241	1
Var 0h	1.638	0.98
Var 12h I row2-row1	0.92419	0.338
Var 12h NI row2-row1	1.03127	1
Var 36h I row2-row1	0.99918	1
Var 36h NI row2-row1	1.02101	1
Var 60h I row2-row1	0.95475	0.952
Var 60h NI row2-row1	1.05079	0.904
Time course 0hI-0hNI	1.01419	1
Time course 12hI-12hNI	0.97465	0.858
Time course 36hI-36hNI	0.82966	0.038
Time course 60hI-60hNI	0.42284	0.006

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)	0.84182	0.157
transgenic ySAMdc/azygous control (breaker)	0.99033	1
transgenic ySAMdc/azygous control (red)	0.85354	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.28839	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1773	0.307
Manapal/WT (break)	0.83711	0.333
Manapal/WT (red)	1.12583	1