Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.17.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15302	0.709
27DAP/17DAP	0.78025	0.354
39DAP/27DAP	1.05135	1
41DAP/39DAP	1.45555	0.243
42DAP/41DAP	1.32371	0.311
43DAP/42DAP	2.27922	0.059
47DAP/43DAP	2.34426	0.321
52DAP/47DAP	1.52134	0.381
57DAP/52DAP	1.00781	0.974

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28219	0.097
17DAP/reference	1.47175	0.047
27DAP/reference	1.35734	0.264
39DAP/reference	1.26823	0.122
41DAP/reference	1.8377	0.014
42DAP/reference	1.66017	0.001
43DAP/reference	1.26127	0.233
47DAP/reference	2.03577	0.001
52DAP/reference	1.79255	0.008
57DAP/reference	1.42609	0.016

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04825	0.858
27DAP/17DAP	1.24722	0.264
39DAP/27DAP	2.39779	0.043
41DAP/39DAP	0.34185	0.013
42DAP/41DAP	4.46991	0.001
43DAP/42DAP	4.34689	0.014
47DAP/43DAP	0.99262	0.93
52DAP/47DAP	1.26468	0.558
57DAP/52DAP	1.14866	0.874
57DAP/7DAP	5.72726	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.60554	0.08
17DAP/reference	0.58187	0.014
27DAP/reference	1.07535	0.371
39DAP/reference	1.05243	0.46
41DAP/reference	0.68574	0.046
42DAP/reference	1.08247	0.686
43DAP/reference	0.89516	0.252
47DAP/reference	1.58561	0.099
52DAP/reference	0.77818	0.115
57DAP/reference	0.43272	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16351	0.794
17DAP/reference	1.59078	0.01
27DAP/reference	1.29979	0.014
39DAP/reference	1.51854	0.013
41DAP/reference	1.44893	0.011
42DAP/reference	1.41358	0.014
43DAP/reference	1.7552	0.014
47DAP/reference	1.31388	0.008
52DAP/reference	1.74138	0.006
57DAP/reference	1.88616	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64034	0.052
17DAP/reference	0.96454	0.462
27DAP/reference	0.49959	0.031
39DAP/reference	0.78968	0.122
41DAP/reference	0.8273	0.148
42DAP/reference	1.96469	0.015
43DAP/reference	1.92737	0.007
47DAP/reference	1.50758	0.031
52DAP/reference	1.74444	0.03
57DAP/reference	0.99795	0.79

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19703	0.966
26DAP/20DAP	0.72134	0.512
34DAP/26DAP	1.11376	1
51DAP/34DAP	2.70144	0.029
52DAP/51DAP	0.94383	1
53DAP/52DAP	5.96911	0.016
55DAP/53DAP	1.17761	0.504
57DAP/55DAP	0.60634	0.057
62DAP/57DAP	0.41417	0.005
68DAP/62DAP	1.21003	0.81
68DAP/14DAP	0.41693	0.056

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.4857	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.15658
Mature Green Tomato/Ripe Tomato	0.18442	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.10522	0.224
Mature Eggplant/Ripe Tomato	0.18087	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03213	1
1-1-2/M82	1.28263	1
12-2/M82	1.06719	1
12-4/M82	0.99961	1
1-3/M82	0.76754	0.501
2-1-1/M82	0.82867	0.465
2-1/M82	1.00228	1
2-6/M82	0.98914	1
3-2/M82	0.0914	0.428
4-1-1/M82	0.87943	1
4-1/M82	1.8037	0.853
4-3-2/M82	0.94633	1
4-3/M82	0.95381	0.72
5-3/M82	0.96577	1
6-2/M82	1.00094	1
6-3/M82	0.99974	1
7-1/M82	0.95298	0.803
7-2/M82	0.9728	0.881
9-3-2/M82	1.2937	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.4229	0.277
IL2-6/WTpooled	0.85658	1
IL7-5/WTpooled	0.73932	1
IL7-3/WTpooled	1.23591	0.362
IL12-4/WTpooled	1.17172	0.522
IL1-4/WTpooled	0.89079	0.415
WT/WTpooled	0.96381	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	1.13421	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06464	0.921
DC3000/delta hrp 6h	1.19511
DC3000/delta hrp 12h	0.83046	1
DC3000/delta hrp 24h	0.89733	0.371

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79314	0.46
DC3000 delta B/DC3000 delta AB	0.77309	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22093	0.254
Exp 36h	N/A	N/A
Exp 60h	1.88924	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01424	1
Var 0h	0.87646	1
Var 12h I row2-row1	1.02013	0.795
Var 12h NI row2-row1	1.04251	1
Var 36h I row2-row1	0.92557	1
Var 36h NI row2-row1	1.09514	1
Var 60h I row2-row1	0.72869	0.285
Var 60h NI row2-row1	1.13154	0.904
Time course 0hI-0hNI	1.04238	0.852
Time course 12hI-12hNI	0.94196	0.285
Time course 36hI-36hNI	0.8813	0.119
Time course 60hI-60hNI	0.92316	0.319

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)	1.58352	0.212
transgenic ySAMdc/azygous control (breaker)	0.60085	0.173
transgenic ySAMdc/azygous control (red)	0.74755	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	1.35882	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.74558	0.172
Manapal/WT (break)	0.89484	1
Manapal/WT (red)	0.91104	0.242