Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02651	0.964
27DAP/17DAP	0.93729	0.902
39DAP/27DAP	0.81764	0.495
41DAP/39DAP	1.40987	0.338
42DAP/41DAP	1.19206	0.85
43DAP/42DAP	0.89209	0.717
47DAP/43DAP	1.00067	0.913
52DAP/47DAP	1.24625	0.651
57DAP/52DAP	0.89031	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96538	0.362
17DAP/reference	0.96898	0.298
27DAP/reference	0.96111	0.349
39DAP/reference	1.03644	0.474
41DAP/reference	1.02142	0.451
42DAP/reference	0.88483	0.006
43DAP/reference	1.05764	0.189
47DAP/reference	0.96309	0.207
52DAP/reference	0.93124	0.167
57DAP/reference	0.83073	0.038

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93561	0.415
27DAP/17DAP	0.9657	0.782
39DAP/27DAP	1.07076	0.56
41DAP/39DAP	1.03558	0.887
42DAP/41DAP	1.02059	0.984
43DAP/42DAP	1.04471	0.446
47DAP/43DAP	1.01787	0.906
52DAP/47DAP	1.01536	0.945
57DAP/52DAP	1.01286	0.957
57DAP/7DAP	1.19952	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89196	0.078
17DAP/reference	0.92588	0.049
27DAP/reference	0.90297	0.014
39DAP/reference	0.93339	0.013
41DAP/reference	0.81961	0.012
42DAP/reference	0.83942	0.016
43DAP/reference	0.87571	0.018
47DAP/reference	0.87679	0.044
52DAP/reference	0.8686	0.019
57DAP/reference	0.79627	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06681	0.36
17DAP/reference	1.0043	1
27DAP/reference	0.93434	0.173
39DAP/reference	0.96947	0.381
41DAP/reference	0.83806	0.018
42DAP/reference	0.82775	0.013
43DAP/reference	1.04459	0.515
47DAP/reference	0.91257	0.09
52DAP/reference	1.07976	0.343
57DAP/reference	1.08422	0.345

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91132	0.135
17DAP/reference	0.91583	0.281
27DAP/reference	0.85665	0.055
39DAP/reference	0.90799	0.035
41DAP/reference	0.88783	0.064
42DAP/reference	0.81987	0.108
43DAP/reference	0.81706	0.076
47DAP/reference	0.93659	0.335
52DAP/reference	0.9945	0.821
57DAP/reference	0.66296	0.025

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04473	0.752
26DAP/20DAP	1.05908	0.924
34DAP/26DAP	0.97504	0.97
51DAP/34DAP	0.98911	0.901
52DAP/51DAP	0.94419	1
53DAP/52DAP	1.01996	0.901
55DAP/53DAP	1.03511	0.964
57DAP/55DAP	1.08932	0.87
62DAP/57DAP	1.18085	0.393
68DAP/62DAP	0.89191	0.668
68DAP/14DAP	1.13437	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84769	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.1476	0.417
Mature Green Tomato/Ripe Tomato	0.87548	0.148
Immature Eggplant/Mature Eggplant	1.13339	0.462
Ripe Pepper/Ripe Tomato	0.50398	0.224
Mature Eggplant/Ripe Tomato	0.55398	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09973	0.877
1-1-2/M82	0.93058	1
12-2/M82	1.11062	1
12-4/M82	0.88182	1
1-3/M82	0.96352	1
2-1-1/M82	1.06836	1
2-1/M82	1.25509	1
2-6/M82	0.93532	1
3-2/M82	1.01661
4-1-1/M82	0.93112	1
4-1/M82	1.01066
4-3-2/M82	0.75217	0.698
4-3/M82	1.04459	1
5-3/M82	1.05822	1
6-2/M82	0.99901	1
6-3/M82	1.00298	1
7-1/M82	0.90677	0.476
7-2/M82	1.10089	1
9-3-2/M82	0.89114	0.449

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.9293	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9267	1
DC3000/delta hrp 6h	0.91132	0.95
DC3000/delta hrp 12h	1.06213	1
DC3000/delta hrp 24h	1.01178	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07424	0.313
DC3000 delta B/DC3000 delta AB	1.00267	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9002	1
Exp 36h	1.587	0.693
Exp 60h	1.33901	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01609	1
Var 0h	0.61783	0.594
Var 12h I row2-row1	1.10894	0.506
Var 12h NI row2-row1	0.93496	0.627
Var 36h I row2-row1	0.77238	0.805
Var 36h NI row2-row1	0.92761	0.706
Var 60h I row2-row1	1.21879	0.562
Var 60h NI row2-row1	1.21164	0.904
Time course 0hI-0hNI	1.09023	0.719
Time course 12hI-12hNI	1.10766	0.385
Time course 36hI-36hNI	1.02611	0.453
Time course 60hI-60hNI	1.1373	0.137

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)	1.05234	0.36
transgenic ySAMdc/azygous control (breaker)	0.76338	0.139
transgenic ySAMdc/azygous control (red)	0.96942	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00863	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.9945	0.789

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66543	0.172
Manapal/WT (break)	0.9169	1
Manapal/WT (red)	0.95905	0.607