Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.72083	0.114
27DAP/17DAP	1.20638	0.849
39DAP/27DAP	1.29352	0.903
41DAP/39DAP	0.84892	0.43
42DAP/41DAP	0.82566	1
43DAP/42DAP	1.17902	0.755
47DAP/43DAP	1.39148	0.856
52DAP/47DAP	1.01686	0.758
57DAP/52DAP	1.61713	0.614

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92357	0.371
17DAP/reference	1.05273	0.239
27DAP/reference	1.01718	0.996
39DAP/reference	1.01838	0.734
41DAP/reference	1.15844	0.122
42DAP/reference	0.89941	0.015
43DAP/reference	0.92834	0.36
47DAP/reference	0.9781	0.418
52DAP/reference	0.90812	0.25
57DAP/reference	0.8332	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.62474	0.774
27DAP/17DAP	1.21326	0.686
39DAP/27DAP	1.03027	1
41DAP/39DAP	0.97008	0.959
42DAP/41DAP	1.06647	0.823
43DAP/42DAP	0.72313	0.076
47DAP/43DAP	1.22842	1
52DAP/47DAP	1.0817	0.835
57DAP/52DAP	1.708	0.161
57DAP/7DAP	1.19357

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03424	0.876
17DAP/reference	1.09384	0.754
27DAP/reference	1.1427	0.664
39DAP/reference	1.16454	0.333
41DAP/reference	0.90621	0.16
42DAP/reference	1.12095	0.534
43DAP/reference	1.0552	0.873
47DAP/reference	1.01523	1
52DAP/reference	1.3079	0.011
57DAP/reference	1.15536	0.308

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95691	0.518
17DAP/reference	0.95968	0.347
27DAP/reference	0.83185	0.155
39DAP/reference	0.82764	0.147
41DAP/reference	0.8559	0.058
42DAP/reference	0.84077	0.042
43DAP/reference	0.91173	0.111
47DAP/reference	0.8913	0.035
52DAP/reference	0.93182	0.156
57DAP/reference	0.982	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02929	1
17DAP/reference	1.08161	0.641
27DAP/reference	1.22695	0.052
39DAP/reference	1.13521	0.157
41DAP/reference	1.14589	0.588
42DAP/reference	1.27944	0.251
43DAP/reference	1.35038	0.254
47DAP/reference	0.94539	0.325
52DAP/reference	1.28362	0.312
57DAP/reference	1.00343	0.424

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01629	1
26DAP/20DAP	1.76162	0.366
34DAP/26DAP	1.12039	1
51DAP/34DAP	0.89342	0.785
52DAP/51DAP	0.69439	0.151
53DAP/52DAP	1.0221	0.876
55DAP/53DAP	1.41196
57DAP/55DAP	1.05176	0.947
62DAP/57DAP	1.27332	0.8
68DAP/62DAP	0.81677	0.641
68DAP/14DAP	0.97139	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.57026	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.47803
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.22873

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	0.7085	0.619
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.95309	1
IL2-6/WTpooled	0.9422	1
IL7-5/WTpooled	0.76968	1
IL7-3/WTpooled	0.96152	1
IL12-4/WTpooled	0.82569	0.71
IL1-4/WTpooled	1.12253	1
WT/WTpooled	1.0727	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	1.11065	0.154

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03006	1
DC3000/delta hrp 6h	1.2161
DC3000/delta hrp 12h	1.172	1
DC3000/delta hrp 24h	1.12187	0.69

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	0.98693	1
Exp 36h	0.90768	0.879
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	1.01485	1
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	2.77148	0.742
Var 36h NI row2-row1	0.79556
Var 60h I row2-row1	0.83661
Var 60h NI row2-row1	1.31143
Time course 0hI-0hNI	0.96381	0.863
Time course 12hI-12hNI	1.05585	0.58
Time course 36hI-36hNI	1.55449	0.063
Time course 60hI-60hNI	3.03508	0.06

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)	1.08036	0.654
transgenic ySAMdc/azygous control (breaker)	1.3837	0.178
transgenic ySAMdc/azygous control (red)	1.17377	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00896	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.10373	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05286	1
Manapal/WT (break)	1.14567	0.381
Manapal/WT (red)	1.15921	0.413