Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.81054	0.29
27DAP/17DAP	0.81035	0.452
39DAP/27DAP	4.68959	0.029
41DAP/39DAP	1.62523	0.339
42DAP/41DAP	0.96486	1
43DAP/42DAP	1.27854	0.937
47DAP/43DAP	1.0916	0.909
52DAP/47DAP	1.48237	0.403
57DAP/52DAP	0.88358	0.79

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93671	0.317
17DAP/reference	1.13624	0.108
27DAP/reference	0.95924	0.395
39DAP/reference	1.16587	0.04
41DAP/reference	1.10839	0.133
42DAP/reference	0.91266	0.056
43DAP/reference	1.34965	0.013
47DAP/reference	1.04546	0.627
52DAP/reference	0.85037	0.115
57DAP/reference	0.8269	0.017

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.43924	0.029
27DAP/17DAP	1.22087	0.373
39DAP/27DAP	1.17823	0.512
41DAP/39DAP	0.77535	0.137
42DAP/41DAP	1.10154	0.927
43DAP/42DAP	3.17745	0.014
47DAP/43DAP	1.43127	0.051
52DAP/47DAP	0.69527	0.122
57DAP/52DAP	0.69137	0.059
57DAP/7DAP	0.85787	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94966	0.224
17DAP/reference	0.91091	0.124
27DAP/reference	1.07634	0.551
39DAP/reference	0.90793	0.17
41DAP/reference	0.83155	0.026
42DAP/reference	0.80195	0.013
43DAP/reference	0.86306	0.021
47DAP/reference	1.00335	1
52DAP/reference	0.88197	0.137
57DAP/reference	0.6851	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03307	1
17DAP/reference	0.89078	0.129
27DAP/reference	1.11129	0.331
39DAP/reference	1.13103	0.956
41DAP/reference	0.77697	0.03
42DAP/reference	0.91905	0.261
43DAP/reference	0.85811	0.087
47DAP/reference	0.98863	0.609
52DAP/reference	0.83253	0.037
57DAP/reference	1.04173	0.957

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89942	0.071
17DAP/reference	0.84721	0.139
27DAP/reference	0.95996	0.337
39DAP/reference	0.87885	0.046
41DAP/reference	0.87302	0.148
42DAP/reference	1.12804	0.576
43DAP/reference	1.05727	0.895
47DAP/reference	0.77581	0.054
52DAP/reference	1.02913	0.928
57DAP/reference	0.65291	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24538	0.117
26DAP/20DAP	0.92855	1
34DAP/26DAP	1.04506	1
51DAP/34DAP	1.20017
52DAP/51DAP	N/A	N/A
53DAP/52DAP	1.17187	0.768
55DAP/53DAP	1.04261	0.838
57DAP/55DAP	0.93426	0.703
62DAP/57DAP	1.03112	1
68DAP/62DAP	0.82684	0.314
68DAP/14DAP	0.67736	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.54006	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.06874	0.017
Immature Eggplant/Mature Eggplant	182.522	0.05
Ripe Pepper/Ripe Tomato	0.03203	0.224
Mature Eggplant/Ripe Tomato	0.17171	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95814	0.961
1-1-2/M82	1.23359	1
12-2/M82	1.2448	1
12-4/M82	0.81824	1
1-3/M82	3.11612	1
2-1-1/M82	0.92696	1
2-1/M82	0.68928	0.322
2-6/M82	1.77028	0.395
3-2/M82	0.49658	0.455
4-1-1/M82	2.35113	0.966
4-1/M82	0.80873
4-3-2/M82	2.16369
4-3/M82	1.43409	1
5-3/M82	1.3962	0.572
6-2/M82	1.28675	0.235
6-3/M82	0.99156	1
7-1/M82	1.6075	0.598
7-2/M82	0.40335	0.426
9-3-2/M82	2.66425

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.45525
IL2-6/WTpooled	1.01565	1
IL7-5/WTpooled	0.70625	1
IL7-3/WTpooled	1.07278	1
IL12-4/WTpooled	0.87758	0.71
IL1-4/WTpooled	1.04625	1
WT/WTpooled	0.98537	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	0.96721	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99554	1
DC3000/delta hrp 6h	0.98845	0.95
DC3000/delta hrp 12h	0.83986	1
DC3000/delta hrp 24h	1.20738	0.37

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00661	1
DC3000 delta B/DC3000 delta AB	1.68787	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17334	0.254
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	0.99118	1
Var 0h	0.55493	0.782
Var 12h I row2-row1	0.87623	0.338
Var 12h NI row2-row1	1.04591	1
Var 36h I row2-row1	0.77588	0.805
Var 36h NI row2-row1	1.08168	1
Var 60h I row2-row1	1.13904	0.562
Var 60h NI row2-row1	0.88639	0.756
Time course 0hI-0hNI	0.89349	0.347
Time course 12hI-12hNI	0.85185	0.101
Time course 36hI-36hNI	1.03482	0.524
Time course 60hI-60hNI	0.55855	0.006

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)	1.57642	0.511
transgenic ySAMdc/azygous control (breaker)	0.45266	0.137
transgenic ySAMdc/azygous control (red)	1.42154	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91605	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.61814	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91094	1
Manapal/WT (break)	0.54512	0.299
Manapal/WT (red)	0.48634	0.181