Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.2.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12612	0.67
27DAP/17DAP	0.81126	0.523
39DAP/27DAP	1.6105	0.183
41DAP/39DAP	0.92481	0.586
42DAP/41DAP	1.46953	0.485
43DAP/42DAP	0.96822	0.91
47DAP/43DAP	0.86215	0.555
52DAP/47DAP	1.48875	0.646
57DAP/52DAP	1.69558	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99948	0.806
17DAP/reference	0.92988	0.097
27DAP/reference	0.86186	0.08
39DAP/reference	0.9604	0.575
41DAP/reference	0.87523	0.039
42DAP/reference	1.00681	1
43DAP/reference	0.99169	0.82
47DAP/reference	1.09449	0.509
52DAP/reference	1.16651	0.056
57DAP/reference	1.0117	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02378	0.975
27DAP/17DAP	1.14874	0.482
39DAP/27DAP	0.6947	0.051
41DAP/39DAP	1.07266	0.849
42DAP/41DAP	1.01509	0.999
43DAP/42DAP	0.98921	0.902
47DAP/43DAP	1.28948	0.52
52DAP/47DAP	0.92339	0.507
57DAP/52DAP	1.01309	0.913
57DAP/7DAP	1.09303	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27784	0.058
17DAP/reference	1.16055	0.07
27DAP/reference	1.10628	0.804
39DAP/reference	1.3109	0.237
41DAP/reference	1.30311	0.02
42DAP/reference	1.20961	0.132
43DAP/reference	1.15284	0.364
47DAP/reference	1.22929	0.165
52DAP/reference	1.24237	0.008
57DAP/reference	1.15002	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87422	0.257
17DAP/reference	0.96688	0.523
27DAP/reference	1.08034	0.507
39DAP/reference	1.02628	1
41DAP/reference	1.10548	0.548
42DAP/reference	0.95493	0.433
43DAP/reference	0.87258	0.105
47DAP/reference	0.85221	0.056
52DAP/reference	0.8319	0.131
57DAP/reference	0.99968	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17377	0.167
17DAP/reference	1.09817	0.326
27DAP/reference	1.20056	0.081
39DAP/reference	1.06662	0.182
41DAP/reference	1.04464	0.939
42DAP/reference	1.20508	0.097
43DAP/reference	1.24987	0.291
47DAP/reference	0.92922	0.335
52DAP/reference	0.97905	0.675
57DAP/reference	1.37093	0.058

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.61325	0.246
26DAP/20DAP	0.87034	1
34DAP/26DAP	1.25624	0.819
51DAP/34DAP	1.93244	0.034
52DAP/51DAP	0.76763	0.151
53DAP/52DAP	1.03264	0.935
55DAP/53DAP	0.77953	0.252
57DAP/55DAP	1.24292	0.492
62DAP/57DAP	0.45486	0.002
68DAP/62DAP	0.88241	0.7
68DAP/14DAP	1.13659	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.29705	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77184	0.23
Mature Green Tomato/Ripe Tomato	1.25651	0.437
Immature Eggplant/Mature Eggplant	0.94707	0.912
Ripe Pepper/Ripe Tomato	3.4524	0.258
Mature Eggplant/Ripe Tomato	1.24246	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.12117	1
12-2/M82	0.73652	N/A
12-4/M82	0.80883	N/A
1-3/M82	N/A	N/A
2-1-1/M82	0.95533	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	1.34549	1
5-3/M82	0.68602	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.11004	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	N/A	N/A
IL2-6/WTpooled	1.03296	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77412	0.418
IL12-4/WTpooled	0.90338	0.543
IL1-4/WTpooled	1.02357	N/A
WT/WTpooled	1.04973	0.805

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	1.00888	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9951	1
DC3000/delta hrp 6h	0.95391	0.95
DC3000/delta hrp 12h	1.01582	1
DC3000/delta hrp 24h	0.77258	0.039

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.53779	N/A
DC3000 delta B/DC3000 delta AB	1.15394	0.332

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88627	1
Exp 36h	1.07444	1
Exp 60h	1.05761	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97017	1
Var 0h	0.87803	0.933
Var 12h I row2-row1	0.8687	0.353
Var 12h NI row2-row1	1.00206	1
Var 36h I row2-row1	1.42859	0.601
Var 36h NI row2-row1	3.43496	1
Var 60h I row2-row1	1.0932	1
Var 60h NI row2-row1	0.89503	0.932
Time course 0hI-0hNI	0.97092	0.861
Time course 12hI-12hNI	0.92521	0.206
Time course 36hI-36hNI	1.03626	0.722
Time course 60hI-60hNI	0.91512	0.161

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)	1.09049	0.278
transgenic ySAMdc/azygous control (breaker)	0.98836	1
transgenic ySAMdc/azygous control (red)	1.01754	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.255	0.061

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85772	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14101	0.14
Manapal/WT (break)	1.40507	0.13
Manapal/WT (red)	1.60482	0.164