Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.19.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.75762	0.19
27DAP/17DAP	1.41355	0.738
39DAP/27DAP	1.14071	0.893
41DAP/39DAP	1.28861	0.478
42DAP/41DAP	1.05913	0.941
43DAP/42DAP	1.25299	0.512
47DAP/43DAP	0.73687	0.269
52DAP/47DAP	2.96226	0.044
57DAP/52DAP	0.71626	0.679

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00127	0.787
17DAP/reference	1.01469	0.675
27DAP/reference	1.01098	0.894
39DAP/reference	1.03398	0.534
41DAP/reference	0.97884	0.542
42DAP/reference	1.05553	0.13
43DAP/reference	1.04486	0.36
47DAP/reference	0.91647	0.05
52DAP/reference	0.81379	0.05
57DAP/reference	0.90615	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94129	0.509
27DAP/17DAP	1.03271	0.915
39DAP/27DAP	1.0206	0.779
41DAP/39DAP	0.99559	0.997
42DAP/41DAP	1.15501	0.539
43DAP/42DAP	0.79499	0.029
47DAP/43DAP	0.90766	0.525
52DAP/47DAP	1.81748	0.048
57DAP/52DAP	1.93448	0.034
57DAP/7DAP	2.94492	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06622
17DAP/reference	N/A	N/A
27DAP/reference	N/A	N/A
39DAP/reference	N/A	N/A
41DAP/reference	0.97197
42DAP/reference	N/A	N/A
43DAP/reference	N/A	N/A
47DAP/reference	1.0855	0.115
52DAP/reference	N/A	N/A
57DAP/reference	1.89516	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06254	0.384
17DAP/reference	0.98327	0.626
27DAP/reference	0.89574	0.167
39DAP/reference	0.81945	0.091
41DAP/reference	0.97657	0.481
42DAP/reference	0.8686	0.098
43DAP/reference	1.00908	0.875
47DAP/reference	1.02318	0.795
52DAP/reference	0.96332	0.351
57DAP/reference	1.00096	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0705
17DAP/reference	1.00769	0.918
27DAP/reference	3.26667	0.056
39DAP/reference	0.95454	0.544
41DAP/reference	N/A	N/A
42DAP/reference	0.83038	0.134
43DAP/reference	0.65767	0.02
47DAP/reference	0.9453	0.383
52DAP/reference	2.40145	0.113
57DAP/reference	1.47156	0.954

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99218	1
26DAP/20DAP	4.90356	0.152
34DAP/26DAP	2.34075	1
51DAP/34DAP	1.24508	0.967
52DAP/51DAP	2.76711	0.033
53DAP/52DAP	0.98937	0.938
55DAP/53DAP	1.26463	0.094
57DAP/55DAP	0.62784	0.067
62DAP/57DAP	1.2443	0.393
68DAP/62DAP	2.25133	0.431
68DAP/14DAP	0.91247	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15535	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	77.2888	0.068
Mature Green Tomato/Ripe Tomato	0.17362	0.017
Immature Eggplant/Mature Eggplant	4.05914	0.05
Ripe Pepper/Ripe Tomato	0.48741
Mature Eggplant/Ripe Tomato	20.8906	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21668	0.742
1-1-2/M82	0.89706	1
12-2/M82	1.39972	1
12-4/M82	1.04071	1
1-3/M82	0.86968	0.501
2-1-1/M82	1.09277
2-1/M82	N/A	N/A
2-6/M82	1.01658	1
3-2/M82	0.65186	1
4-1-1/M82	1.06243	1
4-1/M82	1.20642
4-3-2/M82	0.77351	1
4-3/M82	0.89726	1
5-3/M82	0.99092	1
6-2/M82	0.93573	1
6-3/M82	1.00951	1
7-1/M82	1.06674	1
7-2/M82	1.0543	1
9-3-2/M82	0.23317	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86943
IL2-6/WTpooled	1.17472	0.584
IL7-5/WTpooled	1.16379	0.792
IL7-3/WTpooled	1.07354	1
IL12-4/WTpooled	1.38824	0.525
IL1-4/WTpooled	0.82604	0.834
WT/WTpooled	1.0037	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	1.26925	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05381	0.914
DC3000/delta hrp 6h	0.88239	0.95
DC3000/delta hrp 12h	1.08094	1
DC3000/delta hrp 24h	1.02101	0.743

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.51006	0.042
DC3000 delta B/DC3000 delta AB	1.46007	0.151

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.81561	1
Exp 36h	0.67055	0.504
Exp 60h	0.7978	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02344	1
Var 0h	1.18174	1
Var 12h I row2-row1	1.08105	1
Var 12h NI row2-row1	0.98754	1
Var 36h I row2-row1	0.82955	1
Var 36h NI row2-row1	1.67937	0.482
Var 60h I row2-row1	0.88981	0.439
Var 60h NI row2-row1	1.13814	0.4
Time course 0hI-0hNI	0.94171	0.698
Time course 12hI-12hNI	0.97223	0.836
Time course 36hI-36hNI	0.77733	0.095
Time course 60hI-60hNI	0.91496	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)	1.44039	0.232
transgenic ySAMdc/azygous control (breaker)	1.24553	0.178
transgenic ySAMdc/azygous control (red)	0.93731	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96332	0.069

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.41682	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	N/A	N/A