Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05322	0.977
27DAP/17DAP	1.16696	0.804
39DAP/27DAP	1.18556	0.853
41DAP/39DAP	1.28668	0.728
42DAP/41DAP	1.2805	0.599
43DAP/42DAP	0.84784	0.705
47DAP/43DAP	0.91727	0.701
52DAP/47DAP	1.44265	0.491
57DAP/52DAP	0.87238	0.779

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86274	0.132
17DAP/reference	1.00722	0.764
27DAP/reference	0.92469	0.249
39DAP/reference	0.97617	0.651
41DAP/reference	0.98639	0.814
42DAP/reference	0.91091	0.03
43DAP/reference	1.11002	0.152
47DAP/reference	0.90728	0.027
52DAP/reference	0.79837	0.077
57DAP/reference	0.78241	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04734	0.947
27DAP/17DAP	0.97716	0.887
39DAP/27DAP	1.07887	0.659
41DAP/39DAP	0.866	0.398
42DAP/41DAP	1.10597	0.495
43DAP/42DAP	1.09492	0.513
47DAP/43DAP	1.10003	0.508
52DAP/47DAP	0.93529	0.777
57DAP/52DAP	0.98872	0.823
57DAP/7DAP	1.33601	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82117	0.039
17DAP/reference	0.79694	0.011
27DAP/reference	0.83713	0.01
39DAP/reference	0.85772	0.011
41DAP/reference	0.79368	0.013
42DAP/reference	0.78876	0.01
43DAP/reference	0.73453	0.028
47DAP/reference	0.88697	0.222
52DAP/reference	0.81621	0.035
57DAP/reference	0.75516	0.013

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03125	1
17DAP/reference	1.04162	0.756
27DAP/reference	0.92395	0.317
39DAP/reference	0.82437	0.14
41DAP/reference	0.85968	0.115
42DAP/reference	0.89232	0.261
43DAP/reference	1.10685	0.401
47DAP/reference	0.98154	0.543
52DAP/reference	0.93192	0.259
57DAP/reference	1.24019	0.193

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86187	0.055
17DAP/reference	0.97701	0.668
27DAP/reference	0.84918	0.063
39DAP/reference	0.82952	0.026
41DAP/reference	0.81049	0.04
42DAP/reference	0.77227	0.059
43DAP/reference	0.75559	0.131
47DAP/reference	1.00392	0.646
52DAP/reference	0.89242	0.342
57DAP/reference	0.61615	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88065	0.807
26DAP/20DAP	0.94305	1
34DAP/26DAP	1.1279	1
51DAP/34DAP	0.97059	0.785
52DAP/51DAP	1.20406	0.413
53DAP/52DAP	0.89567	0.732
55DAP/53DAP	1.10318	0.547
57DAP/55DAP	1.0601	0.955
62DAP/57DAP	1.07672	0.935
68DAP/62DAP	0.83362	0.429
68DAP/14DAP	0.64091	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8353	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.92394	0.411
Immature Eggplant/Mature Eggplant	1.89665	0.05
Ripe Pepper/Ripe Tomato	0.49453	1
Mature Eggplant/Ripe Tomato	0.72562	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02786	0.877
1-1-2/M82	0.92831	0.958
12-2/M82	1.07833	1
12-4/M82	0.99807	1
1-3/M82	0.85752	0.441
2-1-1/M82	1.08254
2-1/M82	1.04471
2-6/M82	1.09942	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.04031	1
4-1/M82	0.76249	1
4-3-2/M82	0.94904	1
4-3/M82	0.9397	1
5-3/M82	1.00207	1
6-2/M82	0.8546
6-3/M82	1.04463	1
7-1/M82	N/A	N/A
7-2/M82	0.96351
9-3-2/M82	1.01394	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26766
IL2-6/WTpooled	1.46047	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97858	1
IL12-4/WTpooled	0.78062	0.52
IL1-4/WTpooled	1.09353	1
WT/WTpooled	0.90479	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	0.80428	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99359	1
DC3000/delta hrp 6h	0.60358	0.95
DC3000/delta hrp 12h	1.07742	1
DC3000/delta hrp 24h	0.99217	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53347	0.026
DC3000 delta B/DC3000 delta AB	0.59655	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.09319	1
Exp 60h	1.2564	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07698	1
Var 0h	1.87113	0.98
Var 12h I row2-row1	0.87149	0.627
Var 12h NI row2-row1	0.88758	0.438
Var 36h I row2-row1	1.05735	1
Var 36h NI row2-row1	1.15387	1
Var 60h I row2-row1	1.13971	0.543
Var 60h NI row2-row1	1.07174	0.904
Time course 0hI-0hNI	1.04251	0.719
Time course 12hI-12hNI	1.00035	1
Time course 36hI-36hNI	0.9246	0.171
Time course 60hI-60hNI	0.54381	0.005

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)	1.06846	0.408
transgenic ySAMdc/azygous control (breaker)	1.73822	0.162
transgenic ySAMdc/azygous control (red)	1.06509	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01686	0.317

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13274	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.73794	1
Manapal/WT (break)	1.08168	1
Manapal/WT (red)	1.01366	1