Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.3.10.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16921	0.646
27DAP/17DAP	1.61543	0.49
39DAP/27DAP	1.33611	0.553
41DAP/39DAP	0.81846	0.353
42DAP/41DAP	0.934	1
43DAP/42DAP	9.91585	0.031
47DAP/43DAP	0.27806	0.04
52DAP/47DAP	2.69552	0.406
57DAP/52DAP	1.00675	0.949

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7443	0.064
17DAP/reference	0.74772	0.008
27DAP/reference	0.97773	0.654
39DAP/reference	0.90509	0.228
41DAP/reference	0.72276	0.014
42DAP/reference	1.11762	0.544
43DAP/reference	0.85191	0.08
47DAP/reference	1.06473	0.752
52DAP/reference	1.84653	0.015
57DAP/reference	1.2181	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88312	0.116
27DAP/17DAP	1.7564	0.028
39DAP/27DAP	0.60675	0.062
41DAP/39DAP	1.26398	0.065
42DAP/41DAP	0.9323	0.453
43DAP/42DAP	0.95927	0.709
47DAP/43DAP	1.05425	0.906
52DAP/47DAP	1.22312	0.408
57DAP/52DAP	0.92224	0.339
57DAP/7DAP	1.44976	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84698	0.183
17DAP/reference	1.09904	0.399
27DAP/reference	1.21445	0.035
39DAP/reference	1.04245	0.538
41DAP/reference	1.40123	0.019
42DAP/reference	1.27034	0.014
43DAP/reference	1.04185	0.637
47DAP/reference	0.94121	0.222
52DAP/reference	1.04754	0.832
57DAP/reference	1.15662	0.015

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67236	0.006
17DAP/reference	0.67763	0.018
27DAP/reference	0.95535	0.34
39DAP/reference	0.82054	0.037
41DAP/reference	0.97884	0.432
42DAP/reference	0.94174	0.321
43DAP/reference	0.71389	0.01
47DAP/reference	0.82986	0.015
52DAP/reference	0.83655	0.016
57DAP/reference	0.82683	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00148	0.804
17DAP/reference	1.03094	1
27DAP/reference	1.34404	0.035
39DAP/reference	1.16783	0.03
41DAP/reference	1.1308	0.343
42DAP/reference	1.24883	0.146
43DAP/reference	1.14554	0.343
47DAP/reference	0.9339	0.249
52DAP/reference	1.28242	0.225
57DAP/reference	1.18719	0.135

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22681	0.407
26DAP/20DAP	0.87006	0.512
34DAP/26DAP	1.01086	1
51DAP/34DAP	1.31274	0.511
52DAP/51DAP	0.90836	1
53DAP/52DAP	0.90278	0.386
55DAP/53DAP	1.05131	0.693
57DAP/55DAP	0.96488	0.821
62DAP/57DAP	1.14742	0.833
68DAP/62DAP	1.76156	0.121
68DAP/14DAP	1.78346	0.103

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19598	0.229

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.43301	N/A
Mature Green Tomato/Ripe Tomato	0.5312	0.033
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.1056	0.224
Mature Eggplant/Ripe Tomato	0.1819	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.38712	0.551
1-1-2/M82	1.05906	1
12-2/M82	0.65208	N/A
12-4/M82	1.08617	N/A
1-3/M82	N/A	N/A
2-1-1/M82	2.91368	N/A
2-1/M82	N/A	N/A
2-6/M82	1.15369	0.452
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.78275	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.71096	0.467
6-2/M82	0.44333	N/A
6-3/M82	1.082	1
7-1/M82	N/A	N/A
7-2/M82	1.12306	1
9-3-2/M82	N/A	N/A

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	0.71439	N/A
IL12-4/WTpooled	0.89529	0.71
IL1-4/WTpooled	1.08521	N/A
WT/WTpooled	0.74444	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	2.38749	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08417	0.894
DC3000/delta hrp 6h	1.599	0.392
DC3000/delta hrp 12h	1.15528	1
DC3000/delta hrp 24h	0.95655	0.682

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	1.04856	0.655

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	1.08621	N/A
Var 0h	1.12019	0.936
Var 12h I row2-row1	1.07282	0.654
Var 12h NI row2-row1	0.9972	1
Var 36h I row2-row1	1.16618	1
Var 36h NI row2-row1	1.6255	1
Var 60h I row2-row1	1.2575	0.543
Var 60h NI row2-row1	0.69362	1
Time course 0hI-0hNI	1.00241	1
Time course 12hI-12hNI	1.20476	0.026
Time course 36hI-36hNI	1.97415	0.005
Time course 60hI-60hNI	3.03857	0.009

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)	0.53522	0.299
transgenic ySAMdc/azygous control (breaker)	1.87799	0.248
transgenic ySAMdc/azygous control (red)	0.84493	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94089	0.062

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.73441	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.65735	0.307
Manapal/WT (break)	0.79895	1
Manapal/WT (red)	3.46616	0.126