Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.1.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9203	0.503
27DAP/17DAP	0.99308	1
39DAP/27DAP	0.8822	0.443
41DAP/39DAP	1.23924	0.649
42DAP/41DAP	1.06409	1
43DAP/42DAP	0.86954	0.554
47DAP/43DAP	1.08712	0.856
52DAP/47DAP	1.17941	0.787
57DAP/52DAP	0.99447	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08836	0.587
17DAP/reference	0.95109	0.298
27DAP/reference	1.02861	0.75
39DAP/reference	1.0105	1
41DAP/reference	1.05531	0.171
42DAP/reference	1.20388	0.003
43DAP/reference	1.04748	0.569
47DAP/reference	1.10998	0.044
52DAP/reference	1.36991	0.018
57DAP/reference	1.14439	0.173

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00589	1
27DAP/17DAP	0.99214	0.943
39DAP/27DAP	0.95108	0.304
41DAP/39DAP	0.98465	0.997
42DAP/41DAP	1.03177	0.8
43DAP/42DAP	1.00815	0.699
47DAP/43DAP	1.0261	0.901
52DAP/47DAP	0.96999	0.778
57DAP/52DAP	0.98176	0.73
57DAP/7DAP	0.9225	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13903	0.124
17DAP/reference	1.21354	0.03
27DAP/reference	1.0841	0.035
39DAP/reference	1.03299	0.601
41DAP/reference	1.11858	0.045
42DAP/reference	1.16337	0.012
43DAP/reference	1.10956	0.325
47DAP/reference	1.06415	0.549
52DAP/reference	1.00979	1
57DAP/reference	1.11286	0.17

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17694	0.117
17DAP/reference	1.30501	0.03
27DAP/reference	1.32418	0.03
39DAP/reference	1.53755	0.016
41DAP/reference	1.27193	0.084
42DAP/reference	1.1597	0.214
43DAP/reference	1.20028	0.205
47DAP/reference	1.10065	0.138
52DAP/reference	1.26958	0.012
57DAP/reference	1.39633	0.127

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09707	0.212
17DAP/reference	1.0378	0.784
27DAP/reference	1.02644	0.552
39DAP/reference	1.04118	0.353
41DAP/reference	1.08502	0.296
42DAP/reference	1.16294	0.4
43DAP/reference	1.24124	0.084
47DAP/reference	1.05953	0.61
52DAP/reference	1.01775	0.851
57DAP/reference	1.399	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9727	1
26DAP/20DAP	N/A	N/A
34DAP/26DAP	N/A	N/A
51DAP/34DAP	0.99206	0.927
52DAP/51DAP	1.05752	0.758
53DAP/52DAP	0.97792	0.897
55DAP/53DAP	1.02595	0.848
57DAP/55DAP	0.98179	0.93
62DAP/57DAP	1.36076	0.115
68DAP/62DAP	1.26348	0.398
68DAP/14DAP	1.19985	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0176	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.97654	0.765
Mature Green Tomato/Ripe Tomato	0.99067	0.774
Immature Eggplant/Mature Eggplant	1.24536	0.205
Ripe Pepper/Ripe Tomato	1.29392	1
Mature Eggplant/Ripe Tomato	1.84889

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94772	0.944
1-1-2/M82	0.84181	1
12-2/M82	0.9862	1
12-4/M82	1.0914	1
1-3/M82	0.94793	0.501
2-1-1/M82	0.81309	0.465
2-1/M82	1.0278	1
2-6/M82	0.98341	1
3-2/M82	0.9802	1
4-1-1/M82	0.81059	1
4-1/M82	0.82512	1
4-3-2/M82	0.82598	1
4-3/M82	0.95173	1
5-3/M82	0.9637	0.642
6-2/M82	1.05167	1
6-3/M82	0.94341	0.982
7-1/M82	1.01468	1
7-2/M82	0.98515	0.881
9-3-2/M82	0.89526

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89833	1
IL2-6/WTpooled	0.67605
IL7-5/WTpooled	0.91432	1
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.31764
IL1-4/WTpooled	0.96605
WT/WTpooled	0.91218	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	0.85766

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.54061	1
DC3000/delta hrp 12h	1.00633	1
DC3000/delta hrp 24h	1.03017	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.285	0.042
DC3000 delta B/DC3000 delta AB	1.23216	0.19

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90522	1
Exp 36h	0.80678	0.749
Exp 60h	0.83858	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94873	1
Var 0h	0.88287	0.782
Var 12h I row2-row1	1.29544	0.215
Var 12h NI row2-row1	1.07541	1
Var 36h I row2-row1	1.05425	1
Var 36h NI row2-row1	0.8623	0.584
Var 60h I row2-row1	0.99579	1
Var 60h NI row2-row1	1.11284	0.904
Time course 0hI-0hNI	0.99715	0.988
Time course 12hI-12hNI	1.01014	0.892
Time course 36hI-36hNI	0.94213	0.269
Time course 60hI-60hNI	1.44623	0.033

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)	0.94008	0.454
transgenic ySAMdc/azygous control (breaker)	1.13699	1
transgenic ySAMdc/azygous control (red)	1.31604	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02104	0.35

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09168	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.20516	0.307
Manapal/WT (break)	1.48184	0.183
Manapal/WT (red)	1.14497	1